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From: Dave C. G. H. D. <he...@gm...> - 2010-09-07 18:34:09
|
Hello all, GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts on Monday, 13 September, less than a week from now. This event runs for 4 days and includes: * September 2010 GMOD Meeting - has openings * GMOD Satellite Meetings - has openings * InterMine Workshop - has openings * BioMart Workshop - full (but you can get on the short waiting list) If you haven't already registered, please do so as soon as possible. This will assure you a seat and help us plan meeting logistics. See http://gmod.org/wiki/GMOD_Europe_2010 for details and a registration link. This is the last broadcast reminder I'll send out. Please let me know if you have any questions. Thanks, Dave C. -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://hinv.jp/biocuration2010/ http://gmod.org/wiki/Help_Desk_Feedback |
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From: Lacey-Anne S. <la...@ma...> - 2010-09-01 20:16:46
|
I've created a drupal module that integrates chado fields with views (for those of you not familiar with drupal, the views module allows you to create filterable, sortable tables without programming). This module does not solve the problem of joining data between two databases. Instead, what it does is make chado fields available independent of drupal. Thus each table can only contain data from chado.
Tables that have been implemented: feature, organism, library, cvterm, cv, dbxref, db
There are also default views for feature, organism, library, cvterm, dbxref with sorting, filtering and access control built-in.
These tables do have access to the node ID (necessary to link these tables back to the drupal nodes) through means of a computed field. Essentially, each node ID is retrieved from the database individually using db_query and the chado ID (ie: feature_id, library_id, organism_id) during rendering of the table. Because this field doesn't exist in the database (chado) you can't sort or filter based on the node ID.
Implications of selecting data directly from chado independent of drupal:
1. The views created select directly from chado and cannot include drupal content,
this means:
a) these views will contain data not sync'd with drupal
b) you cannot filter these views by any node fields such as published, user, etc.
c) the node ID fields available are computed fields -meaning a database query is
executed for every row of the table
2. Default views are provided for features, organisms, libraries, cvterms, and dbxrefs
3. Currently only the base table (except in the case of cvterms and dbxrefs which also
implement cv and db respectively) are implemented. Thus you cannot currently access
properties, etc.
4. For Database References, currently only the main feature database reference
(ie: referenced by feature.dbxref_id) is being displayed.
Please comment if this is functionality that you want so that I know whether to implement more tables. Also any feedback would be welcome!
Thanks,
Lacey
PS. Stephen: Is it okay that I set the package=Tripal?
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan
|
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From: Dave C. G. H. D. <he...@gm...> - 2010-08-25 21:02:08
|
Hello all, GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts in less than two weeks. If you are planning on attending and haven't yet registered, then please do so in the next few days. The BioMart Workshop has only a few slots left, and the registration fee for the GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging people to submit topic suggestions for the GMOD Meeting and the GMOD Satellite Meetings. We are also pleased to announce that Jason Swedlow of the University of Dundee will be the guest speaker at the GMOD Meeting. Jason will speak on "The Open Microscopy Environment: Open Informatics for Biological Imaging," a particularly timely topic as many researchers move into image intensive areas such as phenotypes and gene expression, and as high-throughput imaging platforms become available. There is still space available at all 4 events, and registration for the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop is free. Scott Cain and Dave Clements Links: http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/September_2010_GMOD_Meeting http://gmod.org/wiki/Satellite_Meetings_-_GMOD_Europe_2010 http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010 http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010 |
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From: Nicole W. <nlw...@lb...> - 2010-08-23 20:53:47
|
--- ONLY TWO DAYS LEFT TO APPLY --- We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo Hackathon Overview We are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation. The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the Event Discussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion. During the Event Typically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest. Deliverables / Event Results The meeting’s attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically. NESCent This event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program (http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). Links Main GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_Hackathon NESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack |
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From: Dave C. G. H. D. <he...@gm...> - 2010-08-05 04:35:37
|
GMOD Europe 2010 ================ 13-16 September 2010 Cambridge, UK http://gmod.org/wiki/GMOD_Europe_2010 We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction. 2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest. 3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system. 4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches, coffee/tee breaks, and other expenses. Registration for all other events is free, but still required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. For an idea of what goes on at GMOD meetings, see http://gmod.org/wiki/January_2010_GMOD_Meeting. See you in Cambridge! Scott Cain and Dave Clements PS: If you have topics you want to have covered (or you want to cover) at the GMOD Meeting, or at the Satellite Meetings, please add them to the wiki pages, or contact us. We are also asking for guest speaker nominations for the meeting. -- http://gmod.org/wiki/GMOD_News <http://gmod.org/wiki/GMOD_News>http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <he...@gm...> - 2010-08-01 17:03:48
|
We are seeking participants for the GMOD Tools for Evolutionary Biology Hackathon, held November 8-12, 2010 at the US National Evolutionary Synthesis Center (NESCent) in Durham, NC. This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research: 1. Visualization of comparative genomics data 2. Visualization of phylogenetic data and trees 3. Support for population diversity and phenotype data If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply. Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed! How To Apply: Fill out the online application form at http://bit.ly/gmodevohack. Applications are due August 25. About GMOD: GMOD is an intercompatible suite of open-source software components for storing, managing, analyzing, and visualizing genome-scale data. GMOD includes many widely-used software components: GBrowse and JBrowse, both genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a generic and modular database schema; CMap, a comparative map viewer; as well as many other components including Apollo, MAKER, BioMart, InterMine, and Galaxy. We hope to extend the functionality of existing GMOD components, and integrate new components as well. About Hackathons: A hackathon is an intense event at which a group of programmers with different backgrounds and skills collaborate hands-on and face-to-face to develop working code that is of utility to the community as a whole. The mix of people will include domain experts and computer-savvy end-users. More details about the event, its motivation, organization, procedures, and attendees, as well as URLs to the hackathon and related websites are included below. Sincerely, The GMOD EvoHack Organizing Committee (and project affiliations as relevant): Nicole Washington, Chair (LBNL, modENCODE, Phenote) Robert Buels (SGN, Chado NatDiv) Scott Cain (OICR, GMOD) Dave Clements (NESCent, GMOD) Hilmar Lapp (NESCent, Phenoscape, Chado NatDiv) Sheldon McKay (University of Arizona, iPlant, GBrowse_syn) ----------------------------- About the GMOD Evo HackathonOverviewWe are organizing a hackathon to fill critical gaps in the capabilities of the Generic Model Organism Database (GMOD) toolbox that currently limit its utility for evolutionary research. Specifically, we will focus on tools for 1) viewing comparative genomics data; 2) visualizing phylogenomic data; and 3) supporting population diversity data and phenotype annotation.The event will be hosted at NESCent and bring together a group of about 20+ software developers, end-user representatives, and documentation experts who would otherwise not meet. The participants will include key developers of GMOD components that currently lack features critical for emerging evolutionary biology research, developers of informatics tools in evolutionary research that lack GMOD integration, and informatics-savvy biologists who can represent end-user requirements. The event will provide a unique opportunity to infuse the GMOD developer community with a heightened awareness of unmet needs in evolutionary biology that GMOD components have the potential to fill, and for tool developers in evolutionary biology to better understand how best to extend or integrate with already existing GMOD components. Before the EventDiscussion of ideas and sometimes even design actually starts well before the hackathon, on mailing lists, wiki pages, and conference calls set up among accepted attendees. This advance work lays the foundation for participants to be productive from the very first day. This also means that participants should be willing to contribute some time in advance of the hackathon itself to participate in this preparatory discussion.During the EventTypically, hackathon participants use the morning of the first day of the event to organize themselves into working groups of between 3 and 6 people, each with a focused implementation objective. Ideas and objectives are discussed, and attendees coalesce around the projects in which they have the most experience or interest.Deliverables / Event ResultsThe meeting’s attendance, working groups, and outcomes will be fully logged and documented on the GMOD wiki (http://gmod.org). Each working group during the event will typically have its own wiki page, linked from the main EvoHack page, where it documents its minutes and design notes, and provides links to the code and documentation it produces. Also, since GMOD and NESCent are both committed to open source principles, all code and documentation produced by participants during the hackathon must be published under an OSI-approved open source license. As contributions to existing GMOD tools, all hackathon products will most likely satisfy this requirement automatically.NESCentThis event is sponsored by the US National Evolutionary Synthesis Center (NESCent, http://www.nescent.org) through its Informatics Whitepapers program ( http://www.nescent.org/informatics/whitepapers.php). NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries (see http://www.nescent.org/science/proposals.php). LinksMain GMOD EvoHack page, and full proposal: http://gmod.org/wiki/GMOD_Evo_HackathonNESCent: http://www.nescent.org/ GMOD: http://gmod.org Similar past NESCent events, see: http://hackathon.nescent.org/ GMOD hackathon application: http://bit.ly/gmodevohack -- http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback |
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From: Stephen F. <FI...@cl...> - 2010-07-22 02:25:45
|
Dear Tripal User's Group, We have just released a minor revision update for Tripal that fixes several recent bugs that some of you have reported. Thank you to those who reported bugs!! We apologize for the bugs.... You can download this new update from the CUGI website here: http://www.genome.clemson.edu/software/tripal To install this new version please follow these steps: Note: Fixes are backwards compatible and no Drupal style upgrade is necessary. Just copy the new files to your site. 1. Backup your site files before proceeding. 2. Remove the tripal modules from the sites/all/modules directory 3. Remove the theme_tripal theme from the sites/all/themes directory. (If you have customizations you may skip this step). 4. Copy the tripal modules from the updated software to the sites/all/modules directory 5. Copy the tripal_theme from the updated software to the sites/all/themes directory. (If you have customizations you may skip this step). If you have made customizations to your tripal themes you do not need to replace your theme_tripal directory as indicated in steps 3 and 5 above. However, we have made one change to the node-chado_feature.tpl.php template that you may want to copy. To incorporate this change without affecting your existing customizations, copy the following four lines to your template file: <?php # set the title of this page to be the name of the feature. drupal_set_title($feature->featurename); ?> Here is a list of fixes that have occurred: 1. Previously when syncing features, the feature pages were given a title corresponding to the 'name' of the chado feature. This caused several problems. One of which is a title conflict in Drupal if two nodes have the same name. Now, feature pages are given the 'unique name' plus the species name in parentheses as a Drupal node title. We realize this may not be how everyone would like feature pages to appear, so we updated the node-chado_feature.tpl.php template file in the tripal theme to override the title with just the feature 'name'. Users can customize the feature page title however they prefer in this template file. 2. Previously, when syncing features if a feature name and unique name were different the feature would be duplicated in chado. This was a bug. The fix described above also resolves this problem. 3. A recent upgrade to PHP causes some pages to not appear (e.g. organism, library, analysis pages) and others to throw errors. The problem is due to improved stringency in PHP with pass-by-reference parameters in function calls. We fixed many of these. If anyone notices other bugs please feel free to email this list. Regards to all, Stephen |
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From: Stephen F. <FI...@cl...> - 2010-07-14 03:54:57
|
Looking further at this. I realize I made a mistake in my response below. Your original sequence was named 'cu6_0' the duplicated sequence is just named 'cu6'. I reversed them in my mind. Yes, you are correct! This is a bug in Tripal. I just realized what is happening. When the insert function is called in Tripal during syncing it checks to see if the feature exists, but it mistakenly uses the 'name' when querying the 'uniquename' column. Since your uniquename and name are different for the feature, it thinks the feature doesn't exists and it adds it. We will correct this and we'll post a bug fix as quickly as we can. Stephen ________________________________________ From: Stephen Ficklin [FI...@cl...] Sent: Tuesday, July 13, 2010 11:44 PM To: P. Ziarsolo; Meg Staton Cc: GMOD Tripal Subject: Re: [Gmod-tripal] problem infeature sync Hi P?, Meg is correct. Tripal should not be creating features (or duplicating features) during syncing. If this is occurring for you then this is incorrect behavior which we have not seen in our other installations of Tripal. The feature module does have an insert function for adding new features to Chado. This gets called under two conditions: 1) when a new feature is added manually through the Drupal interface, or 2) when creating new nodes programatically. When Tripal "syncs" it is creating new nodes in Drupal programatically, which triggers an insert on the chado database. However, the Tripal code recognizes this and does not try to reinsert the same feature twice. The fact that this is occurring is bizarre. Also, the fact that an "_0" is added to the uniquename is also bizarre since we have not programmed this type of behavior. Would you be willing to share your dataset, or at least a subset, so that we can try to load it at our end to see what's going on? If that's not permissible i understand. If you can share, email me off the mailing list and we can coordinate. Also, what version of Chado are you using? Are you using Chado v1.0 or v1.1? Thanks, Stephen ________________________________________ From: P. Ziarsolo [pzi...@up...] Sent: Tuesday, July 13, 2010 2:34 AM To: Meg Staton Cc: GMOD Tripal Subject: Re: [Gmod-tripal] problem infeature sync Jatorrizko mezua: al., 2010-07-12 07:05 -0700, egilea: Meg Staton > Does the feature with 17381 as the feature_id disappear from the chado > database? No, indeed this feature gets replicated. > > Tripal should not alter the chado database during a feature sync > event. I've scanned the code, and it looks like only select > statements are being used for chado, definitely no inserts. > > As far as not syncing every feature, that is a part of tripal. You > can specify the types of features to sync on the feature admin page; > all other types are ignored. Also, Tripal only looks at features that > are associated with an organism that has been previously synced. cu6 feature is associated with a previously synced organism and is of a type that is synced. > > I think I remember that the "_0" part is something that the gmod perl > load scripts do when you load two features of the same name, but I > could be wrong. > When I load my gff3 to chado, features don't get replicated. It looks like it loads fine. It is only after feature sync of tripal that it gets replicated in the chado database. Previously posted selects are done just before and after the feature sync. Thanks p. > Thanks, > Meg > > -- > Margaret E. Staton > Clemson University Genomics Institute > me...@ya... > 864-656-4643 > > > > > ______________________________________________________________________ > From: P. Ziarsolo <pzi...@up...> > To: GMOD Tripal <gmo...@li...> > Sent: Mon, July 12, 2010 4:06:58 AM > Subject: [Gmod-tripal] problem infeature sync > > Hi, > When I sync features with chado using the feature_sync options of > tripal, I have realized that there are features that althought they > create a accesion in the database, they don't have a feature node of > drupal. > > Looking depper into the problem, I have found that the first feature > that fails has a strange behaviour when features sync. Before Feature > sync: > > chado_melon=# select * from feature where name='cu6'; > feature_id | dbxref_id | organism_id | name | uniquename | residues | > seqlen | md5checksum | type_id | is_analysis | is_obsolete | > timeaccessioned | timelastmodified > ------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+---------------------------- > 17381 | | 13 | cu6 | cu6_0 | | > | | 210 | f | f | 2010-07-09 > 09:18:45.242713 | 2010-07-09 09:18:45.242713 > (1 row) > > after feature sync: > > chado_melon=# select * from feature where name='cu6'; > feature_id | dbxref_id | organism_id | name | uniquename | residues | > seqlen | md5checksum | type_id | is_analysis | is_obsolete | > timeaccessioned | timelastmodified > ------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+---------------------------- > 18260 | | 13 | cu6 | cu6 | | > 0 | | 210 | f | f | 2010-07-12 > 08:03:39.067277 | 2010-07-12 08:03:39.067277 > 17381 | | 13 | cu6 | cu6_0 | | > | | 210 | f | f | 2010-07-09 > 09:18:45.242713 | 2010-07-09 09:18:45.242713 > (2 rows) > > > > I dont know why tripal replicates a feature, The unique difference > between the features is the unique name. Is this a bug or a feature of > tripal? > p. > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-tripal mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-tripal ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-tripal mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
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From: Stephen F. <FI...@cl...> - 2010-07-14 03:44:48
|
Hi P?, Meg is correct. Tripal should not be creating features (or duplicating features) during syncing. If this is occurring for you then this is incorrect behavior which we have not seen in our other installations of Tripal. The feature module does have an insert function for adding new features to Chado. This gets called under two conditions: 1) when a new feature is added manually through the Drupal interface, or 2) when creating new nodes programatically. When Tripal "syncs" it is creating new nodes in Drupal programatically, which triggers an insert on the chado database. However, the Tripal code recognizes this and does not try to reinsert the same feature twice. The fact that this is occurring is bizarre. Also, the fact that an "_0" is added to the uniquename is also bizarre since we have not programmed this type of behavior. Would you be willing to share your dataset, or at least a subset, so that we can try to load it at our end to see what's going on? If that's not permissible i understand. If you can share, email me off the mailing list and we can coordinate. Also, what version of Chado are you using? Are you using Chado v1.0 or v1.1? Thanks, Stephen ________________________________________ From: P. Ziarsolo [pzi...@up...] Sent: Tuesday, July 13, 2010 2:34 AM To: Meg Staton Cc: GMOD Tripal Subject: Re: [Gmod-tripal] problem infeature sync Jatorrizko mezua: al., 2010-07-12 07:05 -0700, egilea: Meg Staton > Does the feature with 17381 as the feature_id disappear from the chado > database? No, indeed this feature gets replicated. > > Tripal should not alter the chado database during a feature sync > event. I've scanned the code, and it looks like only select > statements are being used for chado, definitely no inserts. > > As far as not syncing every feature, that is a part of tripal. You > can specify the types of features to sync on the feature admin page; > all other types are ignored. Also, Tripal only looks at features that > are associated with an organism that has been previously synced. cu6 feature is associated with a previously synced organism and is of a type that is synced. > > I think I remember that the "_0" part is something that the gmod perl > load scripts do when you load two features of the same name, but I > could be wrong. > When I load my gff3 to chado, features don't get replicated. It looks like it loads fine. It is only after feature sync of tripal that it gets replicated in the chado database. Previously posted selects are done just before and after the feature sync. Thanks p. > Thanks, > Meg > > -- > Margaret E. Staton > Clemson University Genomics Institute > me...@ya... > 864-656-4643 > > > > > ______________________________________________________________________ > From: P. Ziarsolo <pzi...@up...> > To: GMOD Tripal <gmo...@li...> > Sent: Mon, July 12, 2010 4:06:58 AM > Subject: [Gmod-tripal] problem infeature sync > > Hi, > When I sync features with chado using the feature_sync options of > tripal, I have realized that there are features that althought they > create a accesion in the database, they don't have a feature node of > drupal. > > Looking depper into the problem, I have found that the first feature > that fails has a strange behaviour when features sync. Before Feature > sync: > > chado_melon=# select * from feature where name='cu6'; > feature_id | dbxref_id | organism_id | name | uniquename | residues | > seqlen | md5checksum | type_id | is_analysis | is_obsolete | > timeaccessioned | timelastmodified > ------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+---------------------------- > 17381 | | 13 | cu6 | cu6_0 | | > | | 210 | f | f | 2010-07-09 > 09:18:45.242713 | 2010-07-09 09:18:45.242713 > (1 row) > > after feature sync: > > chado_melon=# select * from feature where name='cu6'; > feature_id | dbxref_id | organism_id | name | uniquename | residues | > seqlen | md5checksum | type_id | is_analysis | is_obsolete | > timeaccessioned | timelastmodified > ------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+---------------------------- > 18260 | | 13 | cu6 | cu6 | | > 0 | | 210 | f | f | 2010-07-12 > 08:03:39.067277 | 2010-07-12 08:03:39.067277 > 17381 | | 13 | cu6 | cu6_0 | | > | | 210 | f | f | 2010-07-09 > 09:18:45.242713 | 2010-07-09 09:18:45.242713 > (2 rows) > > > > I dont know why tripal replicates a feature, The unique difference > between the features is the unique name. Is this a bug or a feature of > tripal? > p. > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-tripal mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
|
From: P. Z. <pzi...@up...> - 2010-07-13 06:34:35
|
Jatorrizko mezua: al., 2010-07-12 07:05 -0700, egilea: Meg Staton > Does the feature with 17381 as the feature_id disappear from the chado > database? No, indeed this feature gets replicated. > > Tripal should not alter the chado database during a feature sync > event. I've scanned the code, and it looks like only select > statements are being used for chado, definitely no inserts. > > As far as not syncing every feature, that is a part of tripal. You > can specify the types of features to sync on the feature admin page; > all other types are ignored. Also, Tripal only looks at features that > are associated with an organism that has been previously synced. cu6 feature is associated with a previously synced organism and is of a type that is synced. > > I think I remember that the "_0" part is something that the gmod perl > load scripts do when you load two features of the same name, but I > could be wrong. > When I load my gff3 to chado, features don't get replicated. It looks like it loads fine. It is only after feature sync of tripal that it gets replicated in the chado database. Previously posted selects are done just before and after the feature sync. Thanks p. > Thanks, > Meg > > -- > Margaret E. Staton > Clemson University Genomics Institute > me...@ya... > 864-656-4643 > > > > > ______________________________________________________________________ > From: P. Ziarsolo <pzi...@up...> > To: GMOD Tripal <gmo...@li...> > Sent: Mon, July 12, 2010 4:06:58 AM > Subject: [Gmod-tripal] problem infeature sync > > Hi, > When I sync features with chado using the feature_sync options of > tripal, I have realized that there are features that althought they > create a accesion in the database, they don't have a feature node of > drupal. > > Looking depper into the problem, I have found that the first feature > that fails has a strange behaviour when features sync. Before Feature > sync: > > chado_melon=# select * from feature where name='cu6'; > feature_id | dbxref_id | organism_id | name | uniquename | residues | > seqlen | md5checksum | type_id | is_analysis | is_obsolete | > timeaccessioned | timelastmodified > ------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+---------------------------- > 17381 | | 13 | cu6 | cu6_0 | | > | | 210 | f | f | 2010-07-09 > 09:18:45.242713 | 2010-07-09 09:18:45.242713 > (1 row) > > after feature sync: > > chado_melon=# select * from feature where name='cu6'; > feature_id | dbxref_id | organism_id | name | uniquename | residues | > seqlen | md5checksum | type_id | is_analysis | is_obsolete | > timeaccessioned | timelastmodified > ------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+---------------------------- > 18260 | | 13 | cu6 | cu6 | | > 0 | | 210 | f | f | 2010-07-12 > 08:03:39.067277 | 2010-07-12 08:03:39.067277 > 17381 | | 13 | cu6 | cu6_0 | | > | | 210 | f | f | 2010-07-09 > 09:18:45.242713 | 2010-07-09 09:18:45.242713 > (2 rows) > > > > I dont know why tripal replicates a feature, The unique difference > between the features is the unique name. Is this a bug or a feature of > tripal? > p. > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > |
|
From: Meg S. <me...@ya...> - 2010-07-12 14:05:32
|
Does the feature with 17381 as the feature_id disappear from the chado
database?
Tripal should not alter the chado database during a feature sync event. I've
scanned the code, and it looks like only select statements are being used for
chado, definitely no inserts.
As far as not syncing every feature, that is a part of tripal. You can specify
the types of features to sync on the feature admin page; all other types are
ignored. Also, Tripal only looks at features that are associated with an
organism that has been previously synced.
I think I remember that the "_0" part is something that the gmod perl load
scripts do when you load two features of the same name, but I could be wrong.
Thanks,
Meg
--
Margaret E. Staton
Clemson University Genomics Institute
me...@ya...
864-656-4643
________________________________
From: P. Ziarsolo <pzi...@up...>
To: GMOD Tripal <gmo...@li...>
Sent: Mon, July 12, 2010 4:06:58 AM
Subject: [Gmod-tripal] problem infeature sync
Hi,
When I sync features with chado using the feature_sync options of
tripal, I have realized that there are features that althought they
create a accesion in the database, they don't have a feature node of
drupal.
Looking depper into the problem, I have found that the first feature
that fails has a strange behaviour when features sync. Before Feature
sync:
chado_melon=# select * from feature where name='cu6';
feature_id | dbxref_id | organism_id | name | uniquename | residues |
seqlen | md5checksum | type_id | is_analysis | is_obsolete |
timeaccessioned | timelastmodified
------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
17381 | | 13 | cu6 | cu6_0 | |
| | 210 | f | f | 2010-07-09
09:18:45.242713 | 2010-07-09 09:18:45.242713
(1 row)
after feature sync:
chado_melon=# select * from feature where name='cu6';
feature_id | dbxref_id | organism_id | name | uniquename | residues |
seqlen | md5checksum | type_id | is_analysis | is_obsolete |
timeaccessioned | timelastmodified
------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
18260 | | 13 | cu6 | cu6 | |
0 | | 210 | f | f | 2010-07-12
08:03:39.067277 | 2010-07-12 08:03:39.067277
17381 | | 13 | cu6 | cu6_0 | |
| | 210 | f | f | 2010-07-09
09:18:45.242713 | 2010-07-09 09:18:45.242713
(2 rows)
I dont know why tripal replicates a feature, The unique difference
between the features is the unique name. Is this a bug or a feature of
tripal?
p.
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first-- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-tripal mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-tripal
|
|
From: P. Z. <pzi...@up...> - 2010-07-12 08:07:08
|
Hi,
When I sync features with chado using the feature_sync options of
tripal, I have realized that there are features that althought they
create a accesion in the database, they don't have a feature node of
drupal.
Looking depper into the problem, I have found that the first feature
that fails has a strange behaviour when features sync. Before Feature
sync:
chado_melon=# select * from feature where name='cu6';
feature_id | dbxref_id | organism_id | name | uniquename | residues |
seqlen | md5checksum | type_id | is_analysis | is_obsolete |
timeaccessioned | timelastmodified
------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
17381 | | 13 | cu6 | cu6_0 | |
| | 210 | f | f | 2010-07-09
09:18:45.242713 | 2010-07-09 09:18:45.242713
(1 row)
after feature sync:
chado_melon=# select * from feature where name='cu6';
feature_id | dbxref_id | organism_id | name | uniquename | residues |
seqlen | md5checksum | type_id | is_analysis | is_obsolete |
timeaccessioned | timelastmodified
------------+-----------+-------------+------+------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
18260 | | 13 | cu6 | cu6 | |
0 | | 210 | f | f | 2010-07-12
08:03:39.067277 | 2010-07-12 08:03:39.067277
17381 | | 13 | cu6 | cu6_0 | |
| | 210 | f | f | 2010-07-09
09:18:45.242713 | 2010-07-09 09:18:45.242713
(2 rows)
I dont know why tripal replicates a feature, The unique difference
between the features is the unique name. Is this a bug or a feature of
tripal?
p.
|
|
From: Stephen F. <FI...@cl...> - 2010-07-02 14:45:10
|
Hi Peio, When you say you use the path module to redirect from feature name to tripal accession do you mean an external accession (i.e. NCBI accession) or do you mean the Tripal assigned accession? Tripal already uses the path module to provide URLs for Tripal assigned accession. Just want to clarify. I'm not quite sure I understand exactly your search question. But I think you're asking if you can filter searching by feature type? If so, yes you can. There is an option in the Administer -> Tripal Management-> Feature page to 'Set Taxonomy'. Select the check box that says 'Feature Type' and then click the 'Set/Reset Taxonomy for all feature nodes' button. It will add a job to the job queue to set the taxonomy for all nodes. After the job finishes you will then have new advanced searching options on the search page that will let you filter by feature type. Regards, Stephen -----Original Message----- From: P. Ziarsolo [mailto:pzi...@up...] Sent: Friday, July 02, 2010 7:58 AM To: gmo...@li... Subject: [Gmod-tripal] search by feature_type Hi, Finally I could solve the feature accession issue. I have used the path redirect module to redirect from feature name to tripal accession. Now I am having another issue with searching. I would like to have a with all features of a given feature_type. Is this posible? Thanks in advance Peio ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Gmod-tripal mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
|
From: P. Z. <pzi...@up...> - 2010-07-02 11:57:57
|
Hi, Finally I could solve the feature accession issue. I have used the path redirect module to redirect from feature name to tripal accession. Now I am having another issue with searching. I would like to have a with all features of a given feature_type. Is this posible? Thanks in advance Peio |
|
From: Lacey-Anne S. <Lac...@sh...> - 2010-06-28 16:44:27
|
Missed Mailing list ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-2430 Room 3D10 Argriculture Department of Plant Sciences University of Saskatchewan Begin forwarded message: > From: Lacey-Anne Sanderson <Lac...@sh...> > Date: June 28, 2010 10:42:58 AM CST > To: Stephen Ficklin <FI...@cl...> > Subject: Re: SOLVED: Feature Insertion Error; No Feature ID Due to title = name & uniquename > > I definitely agree that the name is more intuitive for the title. But then we run into problems with retrieving the feature_id in the insert, since we can't assume the name is unique and we don't have access to the uniquename anymore. > > Lacey > > ------------------------------------------------------ > Lacey-Anne Sanderson > Bioinformaticist > Pulse Crop Breeding and Genetics > Phone: (306) 966-2430 > Room 3D10 Argriculture > Department of Plant Sciences > University of Saskatchewan > > On 2010-06-28, at 10:17 AM, Stephen Ficklin wrote: > >> Hi Lacey, >> >> Sorry you had this problem. I’m glad you worked around it… >> >> We can make the same fix in the code. Atlhough, I think using the ‘name’ of the feature may still be the preferred way that people refer to features. Dave or Scott (or anyone else), do you have an opinion on what folks would prefer as the page title for a feature? >> >> Drupal may complain about having two nodes with the same title. We’ll have to see. >> >> Thanks, >> Stephen >> >> From: Lacey-Anne Sanderson [mailto:Lac...@sh...] >> Sent: Monday, June 28, 2010 11:31 AM >> To: Stephen Ficklin; GMOD Tripal >> Subject: SOLVED: Feature Insertion Error; No Feature ID Due to title = name & uniquename >> >> Ran into an error over the weekend: >> Unless your uniquename=name, when syncing features you get drupal nodes with no feature id. >> >> This is due to title being assigned the name on line 1380 in tripal_feature_sync_feature ($feature_id) and then the feature id being retrieved using uniquename=title on line 422-424 in chado_feature_insert($node). If name!=uniquename then the select feature_id query fails and the entry in chado_feature has feature_id=0. >> >> In my local copy, I changed the new node in tripal_feature_sync_feature ($feature_id) to have uniquename as the title. This appears to have fixed it. >> >> Lacey >> >> ------------------------------------------------------ >> Lacey-Anne Sanderson >> Bioinformaticist >> Pulse Crop Breeding and Genetics >> Phone: (306) 966-2430 >> Room 3D10 Argriculture >> Department of Plant Sciences >> University of Saskatchewan >> > |
|
From: Scott C. <sc...@sc...> - 2010-06-28 16:35:29
|
Hi Stephen and Lacey, I think that having feature.name as a page title is the most desirable thing, but looking things up by name is liable to cause problems. Even looking up by feature.uniquename can cause problems, but I think you are also specifying organism_id and type_id, so that should be fine. Is it possible to have the page name be feature.name, but look things up by feature.unquename? Scott On Mon, Jun 28, 2010 at 12:17 PM, Stephen Ficklin <FI...@cl...> wrote: > Hi Lacey, > > > > Sorry you had this problem. I’m glad you worked around it… > > > > We can make the same fix in the code. Atlhough, I think using the ‘name’ of > the feature may still be the preferred way that people refer to features. > Dave or Scott (or anyone else), do you have an opinion on what folks would > prefer as the page title for a feature? > > > > Drupal may complain about having two nodes with the same title. We’ll have > to see. > > > > Thanks, > > Stephen > > > > From: Lacey-Anne Sanderson [mailto:Lac...@sh...] > Sent: Monday, June 28, 2010 11:31 AM > To: Stephen Ficklin; GMOD Tripal > Subject: SOLVED: Feature Insertion Error; No Feature ID Due to title = name > & uniquename > > > > Ran into an error over the weekend: > > Unless your uniquename=name, when syncing features you get drupal nodes with > no feature id. > > > > This is due to title being assigned the name on line 1380 > in tripal_feature_sync_feature ($feature_id) and then the feature id being > retrieved using uniquename=title on line 422-424 > in chado_feature_insert($node). If name!=uniquename then the select > feature_id query fails and the entry in chado_feature has feature_id=0. > > > > In my local copy, I changed the new node in tripal_feature_sync_feature > ($feature_id) to have uniquename as the title. This appears to have fixed > it. > > > > Lacey > > > > ------------------------------------------------------ > > Lacey-Anne Sanderson > > Bioinformaticist > > Pulse Crop Breeding and Genetics > > Phone: (306) 966-2430 > > Room 3D10 Argriculture > > Department of Plant Sciences > > University of Saskatchewan > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
|
From: Stephen F. <FI...@cl...> - 2010-06-28 16:18:06
|
Hi Lacey, Sorry you had this problem. I'm glad you worked around it... We can make the same fix in the code. Atlhough, I think using the 'name' of the feature may still be the preferred way that people refer to features. Dave or Scott (or anyone else), do you have an opinion on what folks would prefer as the page title for a feature? Drupal may complain about having two nodes with the same title. We'll have to see. Thanks, Stephen From: Lacey-Anne Sanderson [mailto:Lac...@sh...] Sent: Monday, June 28, 2010 11:31 AM To: Stephen Ficklin; GMOD Tripal Subject: SOLVED: Feature Insertion Error; No Feature ID Due to title = name & uniquename Ran into an error over the weekend: Unless your uniquename=name, when syncing features you get drupal nodes with no feature id. This is due to title being assigned the name on line 1380 in tripal_feature_sync_feature ($feature_id) and then the feature id being retrieved using uniquename=title on line 422-424 in chado_feature_insert($node). If name!=uniquename then the select feature_id query fails and the entry in chado_feature has feature_id=0. In my local copy, I changed the new node in tripal_feature_sync_feature ($feature_id) to have uniquename as the title. This appears to have fixed it. Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-2430 Room 3D10 Argriculture Department of Plant Sciences University of Saskatchewan |
|
From: Lacey-Anne S. <Lac...@sh...> - 2010-06-28 15:30:39
|
Ran into an error over the weekend: Unless your uniquename=name, when syncing features you get drupal nodes with no feature id. This is due to title being assigned the name on line 1380 in tripal_feature_sync_feature ($feature_id) and then the feature id being retrieved using uniquename=title on line 422-424 in chado_feature_insert($node). If name!=uniquename then the select feature_id query fails and the entry in chado_feature has feature_id=0. In my local copy, I changed the new node in tripal_feature_sync_feature ($feature_id) to have uniquename as the title. This appears to have fixed it. Lacey ------------------------------------------------------ Lacey-Anne Sanderson Bioinformaticist Pulse Crop Breeding and Genetics Phone: (306) 966-2430 Room 3D10 Argriculture Department of Plant Sciences University of Saskatchewan |
|
From: Scott C. <sc...@sc...> - 2010-06-17 14:55:20
|
Hello, Thanks to the prep work by Gos Micklem at Cambridge, I am pleased to announce that there will be a two day GMOD community meeting starting on Monday Septermber 13 in Cambridge, England. This meeting occurs immediately prior to the Genome Informatics meeting in Hinxton (for which the abstract deadline is June 25). Registration information for this meeting will be available in a few weeks, though I will accept suggestions for presentations now. Please feel free to forward this to colleagues or mailing lists that you think would be interested in this meeting. I look forward to seeing you in England this Fall. Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Stephen F. <FI...@cl...> - 2010-06-16 21:59:03
|
Hi Lacey.
Thanks so much for your contribution. I'll take a look at it. I think it sounds like something we needed and we will like to incorporate. If we do I'll let you know.
Thanks!
Stephen
On Jun 15, 2010, at 3:57 PM, "Lacey-Anne Sanderson" <Lac...@sh...<mailto:Lac...@sh...>> wrote:
Sorry, pasted my old code (missing a } ). Here is the fixed code:
Changed node_load:
Added the following below $additions->description = $organism->description;
// Add in organism dbxrefs
if ($org_node->organism_id) {
$sql = "SELECT O.common_name,O.organism_id,DBX.accession,DB.description as dbdesc, ".
" DB.db_id, <http://DB.name/> DB.name<http://DB.name> as db_name, DB.urlprefix ".
"FROM {Organism} O ".
" INNER JOIN Organism_dbxref ODBX on O.organism_id = ODBX.organism_id ".
" INNER JOIN Dbxref DBX on DBX.dbxref_id = ODBX.dbxref_id ".
" INNER JOIN DB on DB.db_id = DBX.db_id ".
"WHERE O.organism_id = %d";
$results = db_query($sql,$org_node->organism_id);
$references = array();
$i=0;
while($accession = db_fetch_object($results)){
$references[$i++] = $accession;
}
}
$additions->references = $references;
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan
On 2010-06-15, at 1:49 PM, Lacey-Anne Sanderson wrote:
I ended up needing to display organism dbxrefs (as described in organism_dbxref in chado) on the node page. (I wanted to link each of our organisms to their NCBI taxonomy page) Blow is how I implemented it in case someone else on the mailing list wants to add it to their implementation or you want to add it into the next release of tripal.
Changed node_load:
Added the following below $additions->description = $organism->description;
// Add in organism dbxrefs
if ($org_node->organism_id) {
$sql = "SELECT O.common_name,O.organism_id,DBX.accession,DB.description as dbdesc, ".
" DB.db_id, <http://DB.name/> DB.name<http://DB.name> as db_name, DB.urlprefix ".
"FROM {Organism} O ".
" INNER JOIN Organism_dbxref ODBX on O.organism_id = ODBX.organism_id ".
" INNER JOIN Dbxref DBX on DBX.dbxref_id = ODBX.dbxref_id ".
" INNER JOIN DB on DB.db_id = DBX.db_id ".
"WHERE O.organism_id = %d";
$results = db_query($sql,$org_node->organism_id);
$references = array();
$i=0;
while($accession = db_fetch_object($results)){
$references[$i++] = $accession;
}
}
$additions->references = $references;
Added the following to node-chado_organism.tpl.php
between <div class="content"> and <?php print $content?>
<?php if (!$teaser): ?>
<!-- Control link for the expandableBoxes -->
<br><a id="tripal_expandableBox_toggle_button" onClick="toggleExpandableBoxes()">[-] Collapse All</a><br><br>
<!-- End of Control link for the expandableBoxes -->
<!-- theme_tripal_organism_organism_references -->
<?php
$references = $node->references;
if(count($references) > 0){
?>
<div id="organims-references" class="tripal_organism-info-box">
<div class="tripal_expandableBox"><h3>References</h3></div>
<div class="tripal_expandableBoxContent">
<table>
<tr>
<th>Dababase</th>
<th>Accession</th>
</tr>
<?php
foreach ($references as $result){
?>
<tr>
<td><?php print $result->db_name?></td>
<td><?php if($result->urlprefix){ ?><a href="<?php print $result->urlprefix.$result->accession?>"><?php print $result->accession?></a><?php } else { print $result->accession; } ?></td>
</tr>
<?php } ?>
</table></div></div>
<?php } ?>
<!-- End of theme_tripal_feature_feature_references -->
<?php endif; ?>
Note: This only provides the ability to display dbxrefs already stored in chado. It doesn't provide an web interface for adding dbxrefs to organisms.
Hope this helps somebody,
Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan
|
|
From: Lacey-Anne S. <Lac...@sh...> - 2010-06-15 19:57:46
|
Sorry, pasted my old code (missing a } ). Here is the fixed code:
Changed node_load:
Added the following below $additions->description = $organism->description;
// Add in organism dbxrefs
if ($org_node->organism_id) {
$sql = "SELECT O.common_name,O.organism_id,DBX.accession,DB.description as dbdesc, ".
" DB.db_id, DB.name as db_name, DB.urlprefix ".
"FROM {Organism} O ".
" INNER JOIN Organism_dbxref ODBX on O.organism_id = ODBX.organism_id ".
" INNER JOIN Dbxref DBX on DBX.dbxref_id = ODBX.dbxref_id ".
" INNER JOIN DB on DB.db_id = DBX.db_id ".
"WHERE O.organism_id = %d";
$results = db_query($sql,$org_node->organism_id);
$references = array();
$i=0;
while($accession = db_fetch_object($results)){
$references[$i++] = $accession;
}
}
$additions->references = $references;
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan
On 2010-06-15, at 1:49 PM, Lacey-Anne Sanderson wrote:
> I ended up needing to display organism dbxrefs (as described in organism_dbxref in chado) on the node page. (I wanted to link each of our organisms to their NCBI taxonomy page) Blow is how I implemented it in case someone else on the mailing list wants to add it to their implementation or you want to add it into the next release of tripal.
>
> Changed node_load:
> Added the following below $additions->description = $organism->description;
>
> // Add in organism dbxrefs
> if ($org_node->organism_id) {
> $sql = "SELECT O.common_name,O.organism_id,DBX.accession,DB.description as dbdesc, ".
> " DB.db_id, DB.name as db_name, DB.urlprefix ".
> "FROM {Organism} O ".
> " INNER JOIN Organism_dbxref ODBX on O.organism_id = ODBX.organism_id ".
> " INNER JOIN Dbxref DBX on DBX.dbxref_id = ODBX.dbxref_id ".
> " INNER JOIN DB on DB.db_id = DBX.db_id ".
> "WHERE O.organism_id = %d";
> $results = db_query($sql,$org_node->organism_id);
> $references = array();
> $i=0;
> while($accession = db_fetch_object($results)){
> $references[$i++] = $accession;
> }
}
>
> $additions->references = $references;
>
> Added the following to node-chado_organism.tpl.php
> between <div class="content"> and <?php print $content?>
>
> <?php if (!$teaser): ?>
> <!-- Control link for the expandableBoxes -->
> <br><a id="tripal_expandableBox_toggle_button" onClick="toggleExpandableBoxes()">[-] Collapse All</a><br><br>
> <!-- End of Control link for the expandableBoxes -->
> <!-- theme_tripal_organism_organism_references -->
> <?php
> $references = $node->references;
> if(count($references) > 0){
> ?>
> <div id="organims-references" class="tripal_organism-info-box">
> <div class="tripal_expandableBox"><h3>References</h3></div>
> <div class="tripal_expandableBoxContent">
> <table>
> <tr>
> <th>Dababase</th>
> <th>Accession</th>
> </tr>
> <?php
> foreach ($references as $result){
> ?>
> <tr>
> <td><?php print $result->db_name?></td>
> <td><?php if($result->urlprefix){ ?><a href="<?php print $result->urlprefix.$result->accession?>"><?php print $result->accession?></a><?php } else { print $result->accession; } ?></td>
> </tr>
> <?php } ?>
> </table></div></div>
> <?php } ?>
> <!-- End of theme_tripal_feature_feature_references -->
> <?php endif; ?>
>
> Note: This only provides the ability to display dbxrefs already stored in chado. It doesn't provide an web interface for adding dbxrefs to organisms.
>
> Hope this helps somebody,
> Lacey
>
> ------------------------------------------------------
> Lacey-Anne Sanderson
> Bioinformaticist
> Pulse Crop Breeding and Genetics
> Phone: (306) 966-2430
> Room 3D10 Argriculture
> Department of Plant Sciences
> University of Saskatchewan
>
|
|
From: Lacey-Anne S. <lac...@sh...> - 2010-06-15 19:49:20
|
I ended up needing to display organism dbxrefs (as described in organism_dbxref in chado) on the node page. (I wanted to link each of our organisms to their NCBI taxonomy page) Blow is how I implemented it in case someone else on the mailing list wants to add it to their implementation or you want to add it into the next release of tripal.
Changed node_load:
Added the following below $additions->description = $organism->description;
// Add in organism dbxrefs
if ($org_node->organism_id) {
$sql = "SELECT O.common_name,O.organism_id,DBX.accession,DB.description as dbdesc, ".
" DB.db_id, DB.name as db_name, DB.urlprefix ".
"FROM {Organism} O ".
" INNER JOIN Organism_dbxref ODBX on O.organism_id = ODBX.organism_id ".
" INNER JOIN Dbxref DBX on DBX.dbxref_id = ODBX.dbxref_id ".
" INNER JOIN DB on DB.db_id = DBX.db_id ".
"WHERE O.organism_id = %d";
$results = db_query($sql,$org_node->organism_id);
$references = array();
$i=0;
while($accession = db_fetch_object($results)){
$references[$i++] = $accession;
}
$additions->references = $references;
Added the following to node-chado_organism.tpl.php
between <div class="content"> and <?php print $content?>
<?php if (!$teaser): ?>
<!-- Control link for the expandableBoxes -->
<br><a id="tripal_expandableBox_toggle_button" onClick="toggleExpandableBoxes()">[-] Collapse All</a><br><br>
<!-- End of Control link for the expandableBoxes -->
<!-- theme_tripal_organism_organism_references -->
<?php
$references = $node->references;
if(count($references) > 0){
?>
<div id="organims-references" class="tripal_organism-info-box">
<div class="tripal_expandableBox"><h3>References</h3></div>
<div class="tripal_expandableBoxContent">
<table>
<tr>
<th>Dababase</th>
<th>Accession</th>
</tr>
<?php
foreach ($references as $result){
?>
<tr>
<td><?php print $result->db_name?></td>
<td><?php if($result->urlprefix){ ?><a href="<?php print $result->urlprefix.$result->accession?>"><?php print $result->accession?></a><?php } else { print $result->accession; } ?></td>
</tr>
<?php } ?>
</table></div></div>
<?php } ?>
<!-- End of theme_tripal_feature_feature_references -->
<?php endif; ?>
Note: This only provides the ability to display dbxrefs already stored in chado. It doesn't provide an web interface for adding dbxrefs to organisms.
Hope this helps somebody,
Lacey
------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-2430
Room 3D10 Argriculture
Department of Plant Sciences
University of Saskatchewan
|
|
From: P. Z. <pzi...@up...> - 2010-06-14 07:55:53
|
Hi Stephen, Jatorrizko mezua: or., 2010-06-11 09:31 -0400, egilea: Stephen Ficklin > Hi P?, Peio :) > > We appreciate your feedback! > > Yes, you are correct about the accession number being a combination of a site specific prefix and the feature_id. We agree that this should be fixed. > > In designing Tripal we wanted each feature to have its own site-specific accession. To accomplish this, rather than use the feature_id, as you point out, we really should have a db table entry for the site and assign site-specific accessions by way of the dbxref table and dbxref_id foreign key in the feature table. > > However, it sounds like you would like to use external accessions and have those be used as links into the site. I can see that in some cases folks may want unique site-specific accessions but in other cases would prefer to use external accessions. So, I think what we should do to fix this is the following: > > 1. Correct the use of feature_ids as a component of the site-specific accession. > 2. Make the use of site-specific accessions optional and require users to manually generate accessions for features with a NULL dbxref_id rather than have this occur automatically. > 3. Use the accession provided by the dbxref_id in the feature table as the true accession that get's linked into the site. > > This way, users can have a site-specific accession if they want, or they can have external accessions, or none at all. > This seems good to me. It resolves my issues. Do you have a public code repository to follow the improvements? Thanks !!! p. > I welcome comments from anyone about this idea. But I'll put it on our task list of things to fix. > > Stephen > > > -----Original Message----- > From: P. Ziarsolo [mailto:pzi...@up...] > Sent: Friday, June 11, 2010 5:27 AM > To: gmo...@li... > Subject: [Gmod-tripal] tripal feature accession > > Hi! > I am new to tripal(awesome project). I have found that the accession > used in tripal is a sum of a site specific prefix and chado feature_id. > Is it possible to use the chado's feature's uniquename as accession of > tripal? > > This is useful when you try to access a tripal feature page from an > external application without access to chado database. > I thing is not a good idea to use feature_id as accession because > feature_id is an internal id of chado and it could change in a database > regeneration. Showing this data to users could confuse them if > > Maybe I haven't understand tripal, so I someone could clarify me... > > Thanks in advance > p. > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
|
From: Scott C. <sc...@sc...> - 2010-06-11 14:17:24
|
Hi p, I'll let Stephen and others address the internals of Tripal, but a note about using feature.uniquename to uniquely identify something: be very careful. The value of feature.uniquename is not guaranteed unique; the unique constraint is on the combination of uniquename, type_id and organism_id, so if you wanted to use uniquename, it should really be a concatenation of those three fields. Scott On Fri, Jun 11, 2010 at 5:26 AM, P. Ziarsolo <pzi...@up...> wrote: > Hi! > I am new to tripal(awesome project). I have found that the accession > used in tripal is a sum of a site specific prefix and chado feature_id. > Is it possible to use the chado's feature's uniquename as accession of > tripal? > > This is useful when you try to access a tripal feature page from an > external application without access to chado database. > I thing is not a good idea to use feature_id as accession because > feature_id is an internal id of chado and it could change in a database > regeneration. Showing this data to users could confuse them if > > Maybe I haven't understand tripal, so I someone could clarify me... > > Thanks in advance > p. > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Stephen F. <FI...@cl...> - 2010-06-11 13:49:24
|
Hi P?, We appreciate your feedback! Yes, you are correct about the accession number being a combination of a site specific prefix and the feature_id. We agree that this should be fixed. In designing Tripal we wanted each feature to have its own site-specific accession. To accomplish this, rather than use the feature_id, as you point out, we really should have a db table entry for the site and assign site-specific accessions by way of the dbxref table and dbxref_id foreign key in the feature table. However, it sounds like you would like to use external accessions and have those be used as links into the site. I can see that in some cases folks may want unique site-specific accessions but in other cases would prefer to use external accessions. So, I think what we should do to fix this is the following: 1. Correct the use of feature_ids as a component of the site-specific accession. 2. Make the use of site-specific accessions optional and require users to manually generate accessions for features with a NULL dbxref_id rather than have this occur automatically. 3. Use the accession provided by the dbxref_id in the feature table as the true accession that get's linked into the site. This way, users can have a site-specific accession if they want, or they can have external accessions, or none at all. I welcome comments from anyone about this idea. But I'll put it on our task list of things to fix. Stephen -----Original Message----- From: P. Ziarsolo [mailto:pzi...@up...] Sent: Friday, June 11, 2010 5:27 AM To: gmo...@li... Subject: [Gmod-tripal] tripal feature accession Hi! I am new to tripal(awesome project). I have found that the accession used in tripal is a sum of a site specific prefix and chado feature_id. Is it possible to use the chado's feature's uniquename as accession of tripal? This is useful when you try to access a tripal feature page from an external application without access to chado database. I thing is not a good idea to use feature_id as accession because feature_id is an internal id of chado and it could change in a database regeneration. Showing this data to users could confuse them if Maybe I haven't understand tripal, so I someone could clarify me... Thanks in advance p. ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Gmod-tripal mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
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