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From: Cannon, E. K [C. S] <ekc...@ia...> - 2018-02-15 23:06:38
|
Hi Brandon, I was eager to put the group module to use when developing a method for storing post-composed term, specifically, EQ statements. The table count exploded, so Naama and I settled on a completely different solution<http://gmod.org/wiki/Chado_Post-Composed_Phenotypes>. It's odd that creating a means of generically grouping data objects should be so difficult. Maybe the problem was thinking that grouping should be provided via a module, when instead each module should have its own set of grouping tables, similar to all modules having Xprop, X_relationship, X_dbxref, X_Y tables. (Xgroup, Xgroupprop, Xgroup_relationship...?) Ethy ________________________________ From: Bradford Condon <bra...@gm...> Sent: Tuesday, February 13, 2018 8:48 AM To: GMOD Schema/Chado List Subject: [Gmod-schema] Group module / dbxref Hi all, I am working on an ortholog module that will read in OrthoFinder output and store it in Chado. I’ve read the discussion on the Group Module<http://gmod.org/wiki/Chado_Group_Module> but after reaching out to the authors, they chose to implement ortholog groups for features using feature_<https://laceysanderson.github.io/chado-docs/tables/feature_dbxref.html>dbxref<https://laceysanderson.github.io/chado-docs/tables/feature_dbxref.html>. Do people have recommendations they’d like to share for ortholog groups? I’ve heard three general solutions: Group module - This solution appealed to me but I’m gathering it has issues and may just be too complicated if feature groups are the only goal. dbxref - You create a db with your families, and assign each family an accession in the db. This works well if you’re using established groups hosted on say photozome, but what if i can’t link my groups to established ones and am using an internal db? I guess extra info is stored in cvtermprop for each accession? feature - You create a feature that is the group feature, and associate the members with it. Unfortunately this seems to contradict the definition of a feature. featureprop - you have to annotate each feature as part of the group via feature prop. This seems very problematic. Any input or solutions would be greatly appreciated. Thank you! Bradford Bradford Condon Postdoctoral Scholar, University of Tennessee Knoxville www.bradfordcondon.com<http://www.bradfordcondon.com> |
From: Bradford C. <bra...@gm...> - 2018-02-13 14:49:09
|
Hi all, I am working on an ortholog module that will read in OrthoFinder output and store it in Chado. I’ve read the discussion on the Group Module <http://gmod.org/wiki/Chado_Group_Module> but after reaching out to the authors, they chose to implement ortholog groups for features using feature_ <https://laceysanderson.github.io/chado-docs/tables/feature_dbxref.html>dbxref <https://laceysanderson.github.io/chado-docs/tables/feature_dbxref.html>. Do people have recommendations they’d like to share for ortholog groups? I’ve heard three general solutions: Group module - This solution appealed to me but I’m gathering it has issues and may just be too complicated if feature groups are the only goal. dbxref - You create a db with your families, and assign each family an accession in the db. This works well if you’re using established groups hosted on say photozome, but what if i can’t link my groups to established ones and am using an internal db? I guess extra info is stored in cvtermprop for each accession? feature - You create a feature that is the group feature, and associate the members with it. Unfortunately this seems to contradict the definition of a feature. featureprop - you have to annotate each feature as part of the group via feature prop. This seems very problematic. Any input or solutions would be greatly appreciated. Thank you! Bradford Bradford Condon Postdoctoral Scholar, University of Tennessee Knoxville www.bradfordcondon.com |
From: Sook J. <so...@gm...> - 2018-02-02 21:41:01
|
Hello, Since there is a discussion whether or not to use nd_module for storing phenotype and genotype data in Chado, we wanted to share what we do at GDR, CottonGEN and our other databases. Using the nd_experiment table to link stock and genotype (and project, etc) gave us (and others) a severe performance issue. Lacey came up with the idea of using genotype_call table to link genotype and stock (and project etc). https://github.com/UofS-Pulse-Binfo/nd_genotypes/wiki/How-to-Store-your-Data We adopted this and it has been working very well. We decided to make a similar table to link stock and phenotype tables as well for large-scale phenotype data. We have BIMS Tripal module, which breeders use to store/manage their private data and we anticipate the users (so their data) will grow extensively. Some of them will have phenomics data and the volume of phenotype data will become extensive. The phenotype_call table we create is as follows. phenotype_call_id INT PK phenotype_id INT FK project_id INT FK stock_id INT FK nd_geolocation_id INT FK time TIMESTAMP WITHOUT TIMEZONE This table is basically to link the 'sample' stored in stock table (a specific tree or plot of plants that are being phenotyped) and specific phenotypic value stored in 'phenotype' table. Time field is needed here since the exact phenotyping time can be different for each phenotype for the same sample (this data comes from the FieldBook App that many breeders use). nd_location_id is added here since we don't go through nd_experiment and we need to store the location info of the plant (or animal/insect). I don't think this means that we can get rid of nd module. Nd_experiment table and other associated nd tables are being used for experiments using stocks other than phenotyping and genotyping. Examples are cross, field collection, etc. There are also databases that store various protocols and reagents that are associated with experiments (hence nd_protocol, nd_reagents, etc). For us we need nd_experiment table to store cross data and we don't have data for nd_protocol and nd_reagents. One of the important things that came out of ND discussions were using stock table to store 'samples' and use stock_relationship table to store stock and the sample. There were thoughts to create a separate table such as 'observation_unit' etc. The same principle goes with the project table and project_relationship table to store hierarchical datasets. I think we can think of genotype and phenotype as specific examples of 'experiment' that generate HUGE quantity of data so we use specific linker tables without going through the nd_experiment. It would be nice to open up the conversation to come up with consensus but temporarily we have to use these two tables to speed up loading of our data. Hope it helps! Thanks! Sook and Taein |
From: Scott C. <sc...@sc...> - 2018-01-25 18:45:41
|
Hi Olga, This is more of a Tripal question, so I'm cc'ing the Tripal list. Scott On Thu, Jan 25, 2018 at 7:33 AM, Olga Klonova <Olg...@st...> wrote: > Hi, > > I have a question about a creating a template for the bulk loader. I am > aware of the tutorial on tripal.org, which is absolutely useful, as well > as some posts on the list, but my file seems to be too large to be fit into > a Chado database using the steps from the tutorial. > > In the file each protein has multiple references to external databases > (UniProt, PDB, PFAM) and EC number, information about relevant genes (GI > number, GN, GO), the organism (Taxonomy ID, domain, class, family, genus, > species), and some fields for the protein itself (ID, description, sequence > length). All in all about 20 columns. > > Guess creating a template the usual way (as described in the tutorial) > would lead to a mess, as there are too many fields to use and cross-link. > So I wonder if there is a (recommended) way to load such data into Chado > more efficiently. Would long format help (instead of the wide format, which > is being used now)? Or is it better to split the data into several subsets > and load each independently? Or re-organise the columns somehow? > > Any help would be very much appreciated. > > Olga > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > 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: Olga K. <Olg...@st...> - 2018-01-25 12:49:10
|
Hi, I have a question about a creating a template for the bulk loader. I am aware of the tutorial on tripal.org, which is absolutely useful, as well as some posts on the list, but my file seems to be too large to be fit into a Chado database using the steps from the tutorial. In the file each protein has multiple references to external databases (UniProt, PDB, PFAM) and EC number, information about relevant genes (GI number, GN, GO), the organism (Taxonomy ID, domain, class, family, genus, species), and some fields for the protein itself (ID, description, sequence length). All in all about 20 columns. Guess creating a template the usual way (as described in the tutorial) would lead to a mess, as there are too many fields to use and cross-link. So I wonder if there is a (recommended) way to load such data into Chado more efficiently. Would long format help (instead of the wide format, which is being used now)? Or is it better to split the data into several subsets and load each independently? Or re-organise the columns somehow? Any help would be very much appreciated. Olga |
From: Josh G. <jog...@in...> - 2018-01-11 15:52:33
|
Hi Bradford, Yes, for the data we currently have, the image_cvtermprop approach would work. However, we are starting to see (and we expect to see a lot more) image data of Drosophila embryos at single-cell transcriptome resolution ( http://science.sciencemag.org/content/sci/358/6360/194.full.pdf). It would be very useful to take embryo images with single cell expression data coordinates and cvterms, store that data in Chado, and then take advantage of the geometric functions/operators in PostgreSQL to perform some interesting queries. That said, I'm happy to go the image_cvtermprop route as an initial phase and keep geometric points in mind for possible future implementation. Josh FlyBase On Thu, Jan 11, 2018 at 7:06 AM Bradford Condon <bra...@gm...> wrote: > Hi Josh, > > Thanks so much for your input. > If you’d like the GitHub issue for the eImage module is here, so feel free > to chime in there. > > https://github.com/GMOD/Chado/issues/31 > > It looks like your polygon data consists of a cvterm to map the polygon > to, and a set of coordinates ie `139,116 70,117 73,270 135,212 139,116`. > If thats all correct then it sounds like image_cvtermprop would work, > unless using a table withthe polygon type would work better for your > database? > > > pBradford Condon > Postdoctoral Scholar, University of Tennessee Knoxville > www.bradfordcondon.com > > > > > > On Jan 10, 2018, at 11:50 PM, Josh Goodman <jog...@in...> wrote: > > > > > > * Are you using the eimage table? No > > * have you written eimage linker tables? No > > * Do you have strong images about changing the eimage table itself to > image? No > > > > I would like to request that an image module allow for storing polygon > annotations associated with images and linking those annotations with CV > terms. FlyBase has around a thousand or so images that have been annotated > but are not in our production Chado instance. For example, on > http://flybase.org/reports/FBim0000898, you can mouse over the image and > see the anatomy CV terms associated with particular areas or vice versa. > > > > One open question is whether to store the coordinate data in a prop type > table (e.g. image_cvtermprop) or opt for a table that uses the polygon > geometric type. > > > > I can throw this into a new or existing github issue if you want. > > > > Josh > > > > On Wed, Jan 10, 2018 at 5:37 PM Bradford Condon < > bra...@gm...> wrote: > > Dear Chado community, > > > > We are working on improvements for Chado 1.4 at PAG! You can see the > issues we are working on here. One of the improvements we are making is an > image module from the expression eimage table. > > > > We would like to hear from Chado users who use the expression module's > eimage table. We have a few options, but we are leaning towards keeping > eimage base table as is, and creating the linker tables as _image. This is > the least disruptive option, as the eimage table already exists (even if it > would hold all images, instead of just expression images.) > > > > * Are you using the eimage table? If so, to hold what sort of images? > > * have you written eimage linker tables? If so have you named them > _eimage or _image? > > * Do you have strong images about changing the eimage table itself to > image? > > > > Cheers > > > > Bradford > > > > > > > > Bradford Condon > > Postdoctoral Scholar, University of Tennessee Knoxville > > www.bradfordcondon.com > > > > > > > > > > |
From: Sofia R. <sof...@gm...> - 2018-01-11 14:48:53
|
Hello, I use the eimage table with the chado expression module to allow for the association of cvterms with images. I have not written any eimage linker tables. It would be a bit of a pain, but it would be doable to change everything from eimage to image. Sofia Sent from my iPhone > On Jan 10, 2018, at 8:50 PM, Josh Goodman <jog...@in...> wrote: > > > * Are you using the eimage table? No > * have you written eimage linker tables? No > * Do you have strong images about changing the eimage table itself to image? No > > I would like to request that an image module allow for storing polygon annotations associated with images and linking those annotations with CV terms. FlyBase has around a thousand or so images that have been annotated but are not in our production Chado instance. For example, on http://flybase.org/reports/FBim0000898, you can mouse over the image and see the anatomy CV terms associated with particular areas or vice versa. > > One open question is whether to store the coordinate data in a prop type table (e.g. image_cvtermprop) or opt for a table that uses the polygon geometric type. > > I can throw this into a new or existing github issue if you want. > > Josh > >> On Wed, Jan 10, 2018 at 5:37 PM Bradford Condon <bra...@gm...> wrote: >> Dear Chado community, >> >> We are working on improvements for Chado 1.4 at PAG! You can see the issues we are working on here. One of the improvements we are making is an image module from the expression eimage table. >> >> We would like to hear from Chado users who use the expression module's eimage table. We have a few options, but we are leaning towards keeping eimage base table as is, and creating the linker tables as _image. This is the least disruptive option, as the eimage table already exists (even if it would hold all images, instead of just expression images.) >> >> * Are you using the eimage table? If so, to hold what sort of images? >> * have you written eimage linker tables? If so have you named them _eimage or _image? >> * Do you have strong images about changing the eimage table itself to image? >> >> Cheers >> >> Bradford >> >> >> >> Bradford Condon >> Postdoctoral Scholar, University of Tennessee Knoxville >> www.bradfordcondon.com >> >> >> >> > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Josh G. <jog...@in...> - 2018-01-11 05:24:31
|
* Are you using the eimage table? No * have you written eimage linker tables? No * Do you have strong images about changing the eimage table itself to image? No I would like to request that an image module allow for storing polygon annotations associated with images and linking those annotations with CV terms. FlyBase has around a thousand or so images that have been annotated but are not in our production Chado instance. For example, on http://flybase.org/reports/FBim0000898, you can mouse over the image and see the anatomy CV terms associated with particular areas or vice versa. One open question is whether to store the coordinate data in a prop type table (e.g. image_cvtermprop) or opt for a table that uses the polygon geometric type. I can throw this into a new or existing github issue if you want. Josh On Wed, Jan 10, 2018 at 5:37 PM Bradford Condon <bra...@gm...> wrote: > Dear Chado community, > > We are working on improvements for Chado 1.4 at PAG! You can see the > issues we are working on here <https://github.com/GMOD/Chado/issues>. > One of the improvements we are making is an image module from the > expression eimage table. > > We would like to hear from Chado users who use the expression module's > eimage table. We have a few options, but we are leaning towards keeping > eimage base table as is, and creating the linker tables as _image. This > is the least disruptive option, as the eimage table already exists (even if > it would hold all images, instead of just expression images.) > > * Are you using the eimage table? If so, to hold what sort of images? > * have you written eimage linker tables? If so have you named them > _eimage or _image? > * Do you have strong images about changing the eimage table itself to > image? > > Cheers > > Bradford > > > > Bradford Condon > Postdoctoral Scholar, University of Tennessee Knoxville > www.bradfordcondon.com > > > > > |
From: Bradford C. <bra...@gm...> - 2018-01-10 22:37:19
|
Dear Chado community, We are working on improvements for Chado 1.4 at PAG! You can see the issues we are working on here <https://github.com/GMOD/Chado/issues>. One of the improvements we are making is an image module from the expression eimage table. We would like to hear from Chado users who use the expression module's eimage table. We have a few options, but we are leaning towards keeping eimage base table as is, and creating the linker tables as _image. This is the least disruptive option, as the eimage table already exists (even if it would hold all images, instead of just expression images.) * Are you using the eimage table? If so, to hold what sort of images? * have you written eimage linker tables? If so have you named them _eimage or _image? * Do you have strong images about changing the eimage table itself to image? Cheers Bradford Bradford Condon Postdoctoral Scholar, University of Tennessee Knoxville www.bradfordcondon.com |
From: Scott C. <sc...@sc...> - 2017-12-13 18:36:38
|
Hi All, The pre-PAG hackathon is set to go. It is January 10-11 in San Diego before the Plant and Animal Genomes meeting. The wiki page is here: http://gmod.org/wiki/2018_PAG_Hackathon and while there are several JBrowse/Apollo suggested topics, there are a few Chado topics too, via Bradford Condon: 1. Updating table descriptions to generalize mage to include next-gen sequencing experiments and other possible analyses instead of microarray only 2. Adding a cvalue_id field to the biomaterialprop table, as is done for the natural diversity module. This allows the property values to also utilize a cvterm. Even if you can't make it to the hackathon, please weigh in on these topics, both to their importance (they seem like reasonable things to me) and any gotchas that users might run into. Also, there is a pre-Hackathon call tomorrow at 10 am PT/1 pm ET; please use Zoom to call in if you want to participate: https://lbnl.zoom.us/j/4161956725 Thanks, Scott -- ------------------------------------------------------------------------ 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...> - 2017-11-14 19:04:16
|
What about this? https://groups.io/ On Wed, Jun 28, 2017 at 10:06 PM, Chris Mungall <cjm...@lb...> wrote: > Actually, I found this piece of information: > > It is not well documented but for people > that don't want a google account and want to use the email version of > the list, they have to send an email to: > > <nameofthelist>+su...@go... > > This is not easy to find in the google help. > > > > On Tue, Jun 27, 2017 at 9:00 AM, Chris Mungall <cjm...@lb...> wrote: > >> I hear you. A while ago I looked for alternatives but nothing seemed >> ideal. >> >> On 27 Jun 2017, at 4:39, Karl O. Pinc wrote: >> >> On Mon, Jun 26, 2017 at 5:44 PM Chris Mungall <cjm...@lb... >>>>> <mailto:cjm...@lb...>> wrote: >>>>> >>>> >>> What do people think about kickstarting a new list on google >>>>> groups, merging architecture and schema? >>>>> >>>> >>> The one problem with this is that, unlike a regular email list, >>> google groups requires that you have a google login and so >>> enables all the linking-together and tracking of personal >>> information that goes along with this. >>> >>> I'm not objecting, per-se, but thought it worth a mention. >>> >>> Regards, >>> >>> Karl <ko...@me...> >>> Free Software: "You don't pay back, you pay forward." >>> -- Robert A. Heinlein >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>> >> > |
From: Inderski, B. - A. <Blake.Inderski@ARS.USDA.GOV> - 2017-11-07 19:42:30
|
I'd like to ask for help/feedback on my data assignments to the Chado schema, as shown in the attached PowerPoint sheet. A summary of my data fields: unique ID, source accession, strain/isolate name, strain/isolate source, genotype, author/s, collection location (country/state), collection date (day/month/year), DNA sequence, AA sequence/s, AA sequence name (open reading frame/non-structural protein), AA location. Categories marked as '!null' cannot be left empty. I tried to piece things together as best I could using the general schema structure (http://gmod.org/wiki/Chado_Tables). I ended up using the cvterm table as a catchall for data that lacked a distinct match, since it allows for mixed characters (flexible) and is unique to cv terms (a required field). Please let me know your thoughts and if there are any ways to improve my data categorization. Thanks! Blake This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. |
From: Inderski, B. - A. <Blake.Inderski@ARS.USDA.GOV> - 2017-10-17 21:20:19
|
Greetings! I’m new to Chado and uncertain on how to properly integrate data into the existing Chado schema. My target organism is Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), a single stranded, positive sense RNA virus with a genome approximately 15kb in length. Below are the data fields I’m planning to include, as well as related examples: Metadata Unique ID (automatically generated, sequential identifier) – GB:0000000001 GenBank accession - U40784 Strain/isolate – PRRSv 92V058 Sample isolate source – serum, lymph node, etc. Genotype – Type 1 or Type 2 Author – Doe, J. Sample collection location (state/country) - North Carolina, USA Sample collection date – 30-Dec-2015 Sequencing data Raw DNA sequence – tttggtaatgtgtcaggcattgtggctgtgtgtgtta… Open reading frame (ORF) and non-structural protein (nsp) type – ORF1ab, ORF2, nsp1, nsp12 ORF/nsp location (relative to raw DNA sequence) – 3-501 ORF/nsp translation – MAAATLFLLAGAQHIMVSEAFACKPCFSTHLSD… Any help is much appreciated! Thanks, Blake This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. |
From: Scott C. <sc...@sc...> - 2017-10-12 23:41:16
|
Hi all, This January before PAG on the Wednesday and Thursday before PAG (January 10-11) in San Diego we are planning a GMOD hackathon. We expect that participants will be interested in solving problems/creating solutions related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in another GMOD project, by all means, let us know! We expect this hackathon to overlap with the Tripal hackathon that is on January 11 (I'm pretty sure; right Stephen?) If you are interested in attending this hackathon, please let me know so I can be sure we have an appropriately sized space. And if you're coming for the pre-PAG hackathon, consider staying for PAG, since there is always a lot of GMOD-related content at the meeting! Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
From: Scott C. <sc...@sc...> - 2017-10-12 23:40:40
|
Hi all, This January in San Diego is the annual Plant and Animal Genomes (PAG) meeting (http://www.intlpag.org). As in previous PAGs, there will be several opportunities to present content related to GMOD projects. If you are interested in attending PAG and giving a talk at the GMOD workshop on Wednesday, January 17, please let me know. Your talk can either be about new developments/functionality in existing GMOD software, about how your organization is using the suite of GMOD software to good effect, or about technologies that you think the GMOD community would be interested in hearing about. Please email me directly with a title, an abstract or a vague idea of what you'd like to talk about. Also, if you'd really like to come but are having a hard time coming up with travel funds, please let me know, I might be able to help you with that too (up to a limit of one person anyway). Cheers, Scott -- ------------------------------------------------------------------------ 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...> - 2017-06-28 22:07:01
|
Actually, I found this piece of information: It is not well documented but for people that don't want a google account and want to use the email version of the list, they have to send an email to: <nameofthelist>+su...@go... This is not easy to find in the google help. On Tue, Jun 27, 2017 at 9:00 AM, Chris Mungall <cjm...@lb...> wrote: > I hear you. A while ago I looked for alternatives but nothing seemed ideal. > > On 27 Jun 2017, at 4:39, Karl O. Pinc wrote: > > On Mon, Jun 26, 2017 at 5:44 PM Chris Mungall <cjm...@lb... >>>> <mailto:cjm...@lb...>> wrote: >>>> >>> >> What do people think about kickstarting a new list on google >>>> groups, merging architecture and schema? >>>> >>> >> The one problem with this is that, unlike a regular email list, >> google groups requires that you have a google login and so >> enables all the linking-together and tracking of personal >> information that goes along with this. >> >> I'm not objecting, per-se, but thought it worth a mention. >> >> Regards, >> >> Karl <ko...@me...> >> Free Software: "You don't pay back, you pay forward." >> -- Robert A. Heinlein >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> > |
From: Chris M. <cjm...@lb...> - 2017-06-27 16:02:02
|
I hear you. A while ago I looked for alternatives but nothing seemed ideal. On 27 Jun 2017, at 4:39, Karl O. Pinc wrote: >>> On Mon, Jun 26, 2017 at 5:44 PM Chris Mungall <cjm...@lb... >>> <mailto:cjm...@lb...>> wrote: > >>> What do people think about kickstarting a new list on google >>> groups, merging architecture and schema? > > The one problem with this is that, unlike a regular email list, > google groups requires that you have a google login and so > enables all the linking-together and tracking of personal > information that goes along with this. > > I'm not objecting, per-se, but thought it worth a mention. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema |
From: Karl O. P. <ko...@me...> - 2017-06-27 11:57:35
|
> > On Mon, Jun 26, 2017 at 5:44 PM Chris Mungall <cjm...@lb... > > <mailto:cjm...@lb...>> wrote: > > What do people think about kickstarting a new list on google > > groups, merging architecture and schema? The one problem with this is that, unlike a regular email list, google groups requires that you have a google login and so enables all the linking-together and tracking of personal information that goes along with this. I'm not objecting, per-se, but thought it worth a mention. Regards, Karl <ko...@me...> Free Software: "You don't pay back, you pay forward." -- Robert A. Heinlein |
From: valentin.guignon <gu...@ci...> - 2017-06-27 07:27:05
|
I agree as well. Thx Chris, Val Le 26/06/2017 à 23:49, Josh Goodman a écrit : > +1 > > Josh > > On Mon, Jun 26, 2017 at 5:44 PM Chris Mungall <cjm...@lb... > <mailto:cjm...@lb...>> wrote: > > Looks like these lists are not used so much. Additionally, looks like > sourceforge may start kicking people off lists soon (see my email last > week to gmod-devel). > > What do people think about kickstarting a new list on google groups, > merging architecture and schema? I think there is a need for this. > Earlier today I had someone who was moving their database to chado and > were asking me about ontology loading. Additionally, there is a lot of > fragmented efforts to make a kind of 'chado 2' on top of graph databases > like Neo4J. See http://bit.ly/gmod-graph-database. I know many of us are > probably happy in our individual slack channels for different projects > but I think there is a missed opportunity to work together here. > > What I'm thinking is a new list gmod-architecture on google groups, with > broad contributions welcome, but with a focus on shared architecture > around graph databases. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-architecture mailing list > Gmo...@li... > <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-architecture > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > |
From: Josh G. <jog...@in...> - 2017-06-26 22:23:57
|
+1 Josh On Mon, Jun 26, 2017 at 5:44 PM Chris Mungall <cjm...@lb...> wrote: > Looks like these lists are not used so much. Additionally, looks like > sourceforge may start kicking people off lists soon (see my email last > week to gmod-devel). > > What do people think about kickstarting a new list on google groups, > merging architecture and schema? I think there is a need for this. > Earlier today I had someone who was moving their database to chado and > were asking me about ontology loading. Additionally, there is a lot of > fragmented efforts to make a kind of 'chado 2' on top of graph databases > like Neo4J. See http://bit.ly/gmod-graph-database. I know many of us are > probably happy in our individual slack channels for different projects > but I think there is a missed opportunity to work together here. > > What I'm thinking is a new list gmod-architecture on google groups, with > broad contributions welcome, but with a focus on shared architecture > around graph databases. > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-architecture mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-architecture > |
From: Chris M. <cjm...@lb...> - 2017-06-26 21:44:41
|
Looks like these lists are not used so much. Additionally, looks like sourceforge may start kicking people off lists soon (see my email last week to gmod-devel). What do people think about kickstarting a new list on google groups, merging architecture and schema? I think there is a need for this. Earlier today I had someone who was moving their database to chado and were asking me about ontology loading. Additionally, there is a lot of fragmented efforts to make a kind of 'chado 2' on top of graph databases like Neo4J. See http://bit.ly/gmod-graph-database. I know many of us are probably happy in our individual slack channels for different projects but I think there is a missed opportunity to work together here. What I'm thinking is a new list gmod-architecture on google groups, with broad contributions welcome, but with a focus on shared architecture around graph databases. |
From: Mara K. <mar...@gm...> - 2017-04-19 00:17:40
|
Hi Naama, I am trying to load the FF ontology used to describe samples from the FANTOM5 project: http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology/ff-phase2-140729.obo.txt Thank you so much for all the help, Mara On Mon, Apr 17, 2017 at 7:15 PM Naama Menda <naa...@gm...> wrote: > hi Mara, > yes, this is a command line arg. It requires a number of arguments, it's > listed in the perldoc. > This script loads one ontology at a time, so it expects all terms to have > one prefix > If you have more than one and also references to other ontologies, you > might hit some more roadblocks > Can you send me the obo for the ontology you are trying to load? I could > see if I could make some changes to make this script compatible with it > > best, > -Naama > > > On Mon, Apr 17, 2017 at 4:45 PM Mara Kim <mar...@gm...> wrote: > >> Ok, so I think I have fixed the previous errors. Now I am getting this >> message: >> >> $ perl gmod_load_cvterms.pl -H localhost -D genestation >> /raid/chado/ontology/ff-phase2-140729.obo >> >> Need -s db.name argument! (e.g. GO , PO, etc. >> >> at gmod_load_cvterms.pl line 180. >> >> >> Is this asking for a command line argument? I'm not sure what the proper >> value should be because this ontology spans / includes terms from many >> existing ontologies. >> >> On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> >> wrote: >> >>> >>> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >>> from CPAN) >>> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >>> >>> you should have the chado scripts in a chado/bin directory, and the >>> Bio::GMOD modules in chado/lib/GMOD... >>> then add the path for chado/lib to your $PERL5LIB >>> >>> >>> -Naama >>> >>> >>> >>> >>> >>> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >>> >>>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>>> is no subfolder `Config` which the script seems to be looking for: >>>> >>>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>>> >>>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>>> *Util* >>>> >>>> >>>> Am I missing something? I have version 0.028 installed using cpanm. >>>> >>>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>>> wrote: >>>> >>>> hi Mara, >>>> >>>> where did you install Bio::GMOD ? >>>> If that directory is not in @INC then you need to add it to your >>>> $PERL5LIB >>>> >>>> -Naama >>>> >>>> >>>> >>>> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >>>> >>>> Hi Naama, >>>> >>>> I am trying to use the gmod_load_cvterms.pl script, but I get the >>>> following error: >>>> >>>> $ perl gmod_load_cvterms.pl -H localhost -D genestation >>>> /raid/chado/ontology/ff-phase2-140729.obo >>>> >>>> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >>>> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >>>> /home/kimmm/perl5/lib/perl5/5.10.1 >>>> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >>>> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >>>> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >>>> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >>>> gmod_load_cvterms.pl line 155. >>>> >>>> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >>>> >>>> >>>> I have Bio::GMOD installed. Are there other dependencies that I am >>>> missing? >>>> >>>> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >>>> wrote: >>>> >>>> hi Mara, >>>> >>>> you could try to use the gmod_load_cvterms.pl >>>> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >>>> script >>>> It should handle updating an existing ontology >>>> >>>> >>>> -Naama >>>> >>>> >>>> -- >>>> >>>> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >>>> >>>> I temporarily renamed my `chado` schema to `public`. Now I am getting >>>> a different error: >>>> >>>> $ stag-storenode.pl -d >>>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >>>> ff.xml >>>> >>>> DBD::Pg::st execute failed: ERROR: duplicate key value violates >>>> unique constraint "cvterm_c1" >>>> >>>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>>> >>>> DBD::Pg::st execute failed: ERROR: duplicate key value violates >>>> unique constraint "cvterm_c1" >>>> >>>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>>> >>>> >>>> I am guessing this is because I am loading the Fantom5 ontology, which >>>> references terms from the UBERON ontology. I have already loaded the >>>> UBERON ontology and am using it extensively. Is stag-storenode unable to >>>> resolve this by not recreating duplicated terms? >>>> >>>> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >>>> >>>> Hi, >>>> >>>> When we installed chado we found a number of places >>>> where "public" was hardcoded. >>>> >>>> The places I identify now from a quick review of our notes are: >>>> >>>> initialize.sql >>>> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >>>> ---------------------<snip>-------------------- >>>> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >>>> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >>>> @@ -34,7 +34,8 @@ >>>> >>>> =cut >>>> >>>> -sub default_db_schema { 'public'; } >>>> +#sub default_db_schema { 'public'; } >>>> +sub default_db_schema { 'chado'; } >>>> >>>> sub columns { >>>> my($proto, $dbh, $table) = @_; >>>> ---------------------<snip>-------------------- >>>> >>>> I recall getting chado to install somewhere other than the public >>>> schema to be tedious. >>>> >>>> Regards, >>>> >>>> Karl <ko...@me...> >>>> Free Software: "You don't pay back, you pay forward." >>>> -- Robert A. Heinlein >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> Gmod-schema mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> Gmod-schema mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>>> >>>> |
From: Naama M. <naa...@gm...> - 2017-04-18 00:15:51
|
hi Mara, yes, this is a command line arg. It requires a number of arguments, it's listed in the perldoc. This script loads one ontology at a time, so it expects all terms to have one prefix If you have more than one and also references to other ontologies, you might hit some more roadblocks Can you send me the obo for the ontology you are trying to load? I could see if I could make some changes to make this script compatible with it best, -Naama On Mon, Apr 17, 2017 at 4:45 PM Mara Kim <mar...@gm...> wrote: > Ok, so I think I have fixed the previous errors. Now I am getting this > message: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Need -s db.name argument! (e.g. GO , PO, etc. > > at gmod_load_cvterms.pl line 180. > > > Is this asking for a command line argument? I'm not sure what the proper > value should be because this ontology spans / includes terms from many > existing ontologies. > > On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > >> >> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >> from CPAN) >> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >> >> you should have the chado scripts in a chado/bin directory, and the >> Bio::GMOD modules in chado/lib/GMOD... >> then add the path for chado/lib to your $PERL5LIB >> >> >> -Naama >> >> >> >> >> >> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >> >>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>> is no subfolder `Config` which the script seems to be looking for: >>> >>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>> >>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>> *Util* >>> >>> >>> Am I missing something? I have version 0.028 installed using cpanm. >>> >>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> where did you install Bio::GMOD ? >>> If that directory is not in @INC then you need to add it to your >>> $PERL5LIB >>> >>> -Naama >>> >>> >>> >>> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >>> >>> Hi Naama, >>> >>> I am trying to use the gmod_load_cvterms.pl script, but I get the >>> following error: >>> >>> $ perl gmod_load_cvterms.pl -H localhost -D genestation >>> /raid/chado/ontology/ff-phase2-140729.obo >>> >>> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >>> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.1 >>> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >>> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >>> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >>> gmod_load_cvterms.pl line 155. >>> >>> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >>> >>> >>> I have Bio::GMOD installed. Are there other dependencies that I am >>> missing? >>> >>> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> you could try to use the gmod_load_cvterms.pl >>> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >>> script >>> It should handle updating an existing ontology >>> >>> >>> -Naama >>> >>> >>> -- >>> >>> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >>> >>> I temporarily renamed my `chado` schema to `public`. Now I am getting a >>> different error: >>> >>> $ stag-storenode.pl -d >>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >>> ff.xml >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> >>> I am guessing this is because I am loading the Fantom5 ontology, which >>> references terms from the UBERON ontology. I have already loaded the >>> UBERON ontology and am using it extensively. Is stag-storenode unable to >>> resolve this by not recreating duplicated terms? >>> >>> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >>> >>> Hi, >>> >>> When we installed chado we found a number of places >>> where "public" was hardcoded. >>> >>> The places I identify now from a quick review of our notes are: >>> >>> initialize.sql >>> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >>> ---------------------<snip>-------------------- >>> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >>> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >>> @@ -34,7 +34,8 @@ >>> >>> =cut >>> >>> -sub default_db_schema { 'public'; } >>> +#sub default_db_schema { 'public'; } >>> +sub default_db_schema { 'chado'; } >>> >>> sub columns { >>> my($proto, $dbh, $table) = @_; >>> ---------------------<snip>-------------------- >>> >>> I recall getting chado to install somewhere other than the public >>> schema to be tedious. >>> >>> Regards, >>> >>> Karl <ko...@me...> >>> Free Software: "You don't pay back, you pay forward." >>> -- Robert A. Heinlein >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>> >>> |
From: Mara K. <mar...@gm...> - 2017-04-17 21:01:08
|
This is further complicated by the fact that the ids use multiple db.names On Mon, Apr 17, 2017 at 3:44 PM Mara Kim <mar...@gm...> wrote: > Ok, so I think I have fixed the previous errors. Now I am getting this > message: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Need -s db.name argument! (e.g. GO , PO, etc. > > at gmod_load_cvterms.pl line 180. > > > Is this asking for a command line argument? I'm not sure what the proper > value should be because this ontology spans / includes terms from many > existing ontologies. > > On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > >> >> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >> from CPAN) >> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >> >> you should have the chado scripts in a chado/bin directory, and the >> Bio::GMOD modules in chado/lib/GMOD... >> then add the path for chado/lib to your $PERL5LIB >> >> >> -Naama >> >> >> >> >> >> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >> >>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>> is no subfolder `Config` which the script seems to be looking for: >>> >>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>> >>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>> *Util* >>> >>> >>> Am I missing something? I have version 0.028 installed using cpanm. >>> >>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> where did you install Bio::GMOD ? >>> If that directory is not in @INC then you need to add it to your >>> $PERL5LIB >>> >>> -Naama >>> >>> >>> >>> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >>> >>> Hi Naama, >>> >>> I am trying to use the gmod_load_cvterms.pl script, but I get the >>> following error: >>> >>> $ perl gmod_load_cvterms.pl -H localhost -D genestation >>> /raid/chado/ontology/ff-phase2-140729.obo >>> >>> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >>> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.1 >>> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >>> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >>> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >>> gmod_load_cvterms.pl line 155. >>> >>> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >>> >>> >>> I have Bio::GMOD installed. Are there other dependencies that I am >>> missing? >>> >>> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> you could try to use the gmod_load_cvterms.pl >>> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >>> script >>> It should handle updating an existing ontology >>> >>> >>> -Naama >>> >>> >>> -- >>> >>> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >>> >>> I temporarily renamed my `chado` schema to `public`. Now I am getting a >>> different error: >>> >>> $ stag-storenode.pl -d >>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >>> ff.xml >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> >>> I am guessing this is because I am loading the Fantom5 ontology, which >>> references terms from the UBERON ontology. I have already loaded the >>> UBERON ontology and am using it extensively. Is stag-storenode unable to >>> resolve this by not recreating duplicated terms? >>> >>> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >>> >>> Hi, >>> >>> When we installed chado we found a number of places >>> where "public" was hardcoded. >>> >>> The places I identify now from a quick review of our notes are: >>> >>> initialize.sql >>> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >>> ---------------------<snip>-------------------- >>> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >>> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >>> @@ -34,7 +34,8 @@ >>> >>> =cut >>> >>> -sub default_db_schema { 'public'; } >>> +#sub default_db_schema { 'public'; } >>> +sub default_db_schema { 'chado'; } >>> >>> sub columns { >>> my($proto, $dbh, $table) = @_; >>> ---------------------<snip>-------------------- >>> >>> I recall getting chado to install somewhere other than the public >>> schema to be tedious. >>> >>> Regards, >>> >>> Karl <ko...@me...> >>> Free Software: "You don't pay back, you pay forward." >>> -- Robert A. Heinlein >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Gmod-schema mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema >>> >>> |
From: Mara K. <mar...@gm...> - 2017-04-17 20:45:15
|
Ok, so I think I have fixed the previous errors. Now I am getting this message: $ perl gmod_load_cvterms.pl -H localhost -D genestation /raid/chado/ontology/ff-phase2-140729.obo Need -s db.name argument! (e.g. GO , PO, etc. at gmod_load_cvterms.pl line 180. Is this asking for a command line argument? I'm not sure what the proper value should be because this ontology spans / includes terms from many existing ontologies. On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > > Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get from > CPAN) > https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD > > you should have the chado scripts in a chado/bin directory, and the > Bio::GMOD modules in chado/lib/GMOD... > then add the path for chado/lib to your $PERL5LIB > > > -Naama > > > > > > On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: > >> Ok, so I checked the location of my Bio::GMOD and I noticed that there is >> no subfolder `Config` which the script seems to be looking for: >> >> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >> >> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >> *Util* >> >> >> Am I missing something? I have version 0.028 installed using cpanm. >> >> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >> wrote: >> >> hi Mara, >> >> where did you install Bio::GMOD ? >> If that directory is not in @INC then you need to add it to your >> $PERL5LIB >> >> -Naama >> >> >> >> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >> >> Hi Naama, >> >> I am trying to use the gmod_load_cvterms.pl script, but I get the >> following error: >> >> $ perl gmod_load_cvterms.pl -H localhost -D genestation >> /raid/chado/ontology/ff-phase2-140729.obo >> >> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >> /home/kimmm/perl5/lib/perl5/5.10.1 >> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >> gmod_load_cvterms.pl line 155. >> >> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >> >> >> I have Bio::GMOD installed. Are there other dependencies that I am >> missing? >> >> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >> wrote: >> >> hi Mara, >> >> you could try to use the gmod_load_cvterms.pl >> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >> script >> It should handle updating an existing ontology >> >> >> -Naama >> >> >> -- >> >> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >> >> I temporarily renamed my `chado` schema to `public`. Now I am getting a >> different error: >> >> $ stag-storenode.pl -d >> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >> ff.xml >> >> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >> constraint "cvterm_c1" >> >> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >> >> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >> constraint "cvterm_c1" >> >> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >> >> >> I am guessing this is because I am loading the Fantom5 ontology, which >> references terms from the UBERON ontology. I have already loaded the >> UBERON ontology and am using it extensively. Is stag-storenode unable to >> resolve this by not recreating duplicated terms? >> >> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >> >> Hi, >> >> When we installed chado we found a number of places >> where "public" was hardcoded. >> >> The places I identify now from a quick review of our notes are: >> >> initialize.sql >> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >> ---------------------<snip>-------------------- >> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >> @@ -34,7 +34,8 @@ >> >> =cut >> >> -sub default_db_schema { 'public'; } >> +#sub default_db_schema { 'public'; } >> +sub default_db_schema { 'chado'; } >> >> sub columns { >> my($proto, $dbh, $table) = @_; >> ---------------------<snip>-------------------- >> >> I recall getting chado to install somewhere other than the public >> schema to be tedious. >> >> Regards, >> >> Karl <ko...@me...> >> Free Software: "You don't pay back, you pay forward." >> -- Robert A. Heinlein >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> >> |