Re: [mart-dev] BioMart / ProServer
Hi! On 5 November 2010 08:01, Charles Imbusch char...@imbusch.net wrote: Maybe I missed something, but I thought ProServer is the common DAS server to work with BioMart. As far as I understand it, ProServer works with BioMart and there are examples on how to customise it for a mart. However, in section 6.10 DAS Server of the BioMart 0.7 documentation (http://www.biomart.org/user-docs.pdf) it gives examples that work just out of the box. It might just be the case that a ProServer installation allows you a more versatile approach towards solving your problem. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] BioMart / ProServer
Hi! On 4 November 2010 10:29, Charles Imbusch char...@imbusch.net wrote: Does maybe an existing example configuration for BioMart/ProServer exist? Is the build-in DAS-server of BioMart not sufficient enough for you? It actually works fairly well. If you want to plug-in a DAS-track into the Ensembl-browser, you need to make some modifications though. You have to provide a SOURCES command as well, which has been hacked into BioMart 0.7 by me: https://github.com/joejimbo/biomart-plus-extras A lot is hardcoded, but I am sure you could modify it to your needs. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Command Based marteditor
Hi! You might be interested in MartScript, http://github.com/joejimbo/MartScript, which can be used to automatically create Ensembl (and related) marts. I do not know your database structure, but perhaps it would work for you with some minor modifications as well. The major downside of using MartScript right now is obvious: I have been too lazy to document it properly yet. If you have a go at it, please let me know and perhaps we can figure out to get it working together. Are you around at Genome Informatics next week? We could have a chat about it too. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Command Based marteditor
Hi, On 8 September 2010 11:51, a.has...@har.mrc.ac.uk wrote: File = Naive File = import File = update all File = export Do you reckon that MartScript will help us? 'Naive' is not supported as such, but you could have a look at the Java code and implement it yourself. It is fairly straightforward, because I just call MartEditor code from within MartScript when mimicking MartBuilder/MartEditor functionality. The other steps would work though. I am going to IMGC, Crete, Greece in October. Please let me know if you will be there then we can discuss this further. Thanks. Unfortunately, I am not going there. Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Using Biomart + WSDL + java
On 22 March 2010 12:09, Richard Holland holl...@eaglegenomics.com wrote: REST is only suitable for queries with a small number of filters or attributes that can fit within the maximum length of an HTTP URL. It is also unsuitable where large numbers of values need to be specified in a filter, e.g. by uploading a file of IDs. I see. Yes, REST would be unsuitable for those cases. BW, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Homogeneous filter-set across all species
Hello, Is it possible to have the same set of filters for every species? I have noticed that for some species, where we cannot provide data for, the 'ID list limit' filter is missing. There is still an entry for 'Limit to genes...' though, which of course returns an empty result set for those species. It would be nice to see the 'ID list limit' filter too, even though it would be not functional. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] BioMart 0.8: User Interface
Hello, We are about to get the mart we built up and running soon and while we were developing it, but also now as it is getting finalised, I kept asking colleagues whether they could give it a try and test the interface a little bit. Whilst the purpose was to find possible inconsistent data in our mart and to check the performance of database queries, *all* participants were simply overwhelmed by the mart user-interface. Even though I find the interface accessible myself, I have to admit that I spent quite some time with BioMart now, so my opinion is certainly not unbiased anymore. If it is not too late, it would be great if BioMart 0.8 could be tested for usability on non-computer scientists/non-bioinformaticians before it is released. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] BioMart 0.8: User Interface
Hi! I am looking forward to BioMart 0.8 then.. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Installing Biomart 0.6 on 64 bit linux
On 17 March 2010 17:15, nnde...@ebi.ac.uk wrote: Has anyone been able to successfully do this? Any ideas how i can go about this please? BioMart 0.7 runs fine in 64 bit environments, both Linux and OSX. I just encountered some troubles under the old OSX 10.5, where either Perl or the MySQL server were only 32 bit. However, if you do not mix 32/64 bit installations, then you should be fine really. BW, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Suggestion: Exportables over Multiple Attribute Pages
Hello, I am just working on the DAS representation of our data again and came across the annoying message: 'Attributes from multiple attribute pages are not allowed', because I mixed attributes from two feature pages in an exportable. Basically, I had the exportable set to include all of our newly added features and then added the extra feature 'external_gene_id' (a.k.a. Associated Gene Name) of our Ensembl mart. It would be nice if the new upcoming BioMart would support this. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Attaching BioMart DAS Sources to the Ensembl Genome Browser
Hello, I wrote a patch for the current BioMart version, so that one can automagically attach BioMart DAS-tracks to the Ensembl Genome browser. The patch files and a short description on the topic can be found here: http://bergmanlab.smith.man.ac.uk/?p=43 Perhaps this is useful to someone else too. BW, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Exception in MartBuilder when generating SQL-file
Hello, I have added some data to our customised Ensembl mart and I am trying to rebuild it now. However, when I update all schemas in MartBuilder, then accept all changes and finally try to generate the SQL for the mart, the exceptions as shown below occur. Please note that even though the top of the call stacks says 'MartScript' rather than 'MartBuilder', it is the same underlying code of MartBuilder that gets executed. I just wrote a scripting front-end that takes me through the mart creation process, which I would otherwise have to do by hand. At first I thought there was a network connection problem regarding the MySQL database, but since this exception reoccurred, I begin to doubt that. Could this be related to the extended amount of time MartBuilder needs to pick up the tables that I have added to Ensembl? It takes about 7h for MartBuilder to calculate the database changes once I have clicked 'Update all schemas'. com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception: ** BEGIN NESTED EXCEPTION ** java.io.EOFException STACKTRACE: java.io.EOFException at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) at com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79) at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) at com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79) at com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) at org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773) at org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787) at org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818) at org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) at org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662) at org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273) at org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) at org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) ** END NESTED EXCEPTION ** Last packet sent to the server was 204460 ms ago. at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) at com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) at com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79) at com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) at com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) at com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79) at com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) at org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java:1773) at org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema.java:1787) at org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1818) at org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) at org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter.java:1662) at org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterpreter.java:273) at org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) at org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) Woops.. the following exception occurred during the script's exception: java.sql.SQLException: No
[mart-dev] DAS Request: Where does it get its filters from?
Hello, When I am running a simple DAS request, such as: http://myhost/biomart/das/default__hsapiens_gene_ensembl__ensembl_das_chr/features?segment=13:31787617,31871805 I am getting a XML Parsing Error: not well-formed message, which includes the following line: LINK href=http://myhost/biomart/martview?VIRTUALSCHEMANAME=defaultATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.mydata_1090FILTERS=hsapiens_gene_ensembl.default.filters.ensembl_gene_id.ENSG0187676VISIBLEPANEL=resultspanel/LINK The attribute mydata_1090 is not present in my mart (it has a different numerical part), so I am wondering where BioMart gets this data from. I am also surprised that an extra attribute besides the gene_id is included at all. Why would that be the case? DAS queries have worked before for my mart and I am not sure what I have changed that causes this behaviour. I would appreciate if someone could point out to me what to look for. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] SQL zombies
Hello, I picked up some weird MySQL behaviour when querying my local mart. Basically, there would be entries left in the MySQL process list which resemble process zombies on the operating system level. For example, 'show processlist;' would display the following information: Id, db, Command, Time, State, Info 16538, NULL, Query, 0, NULL, show processlist 16543, ensembl_mart_56, Sleep, 471, , NULL 17100, biomart, Sleep, 10, , NULL 17101, ensembl_mart_56, Query, 10, Sending data, SELECT main.stable_id_1023, ... Apparently, the thread 17100 is started at the same time as the query with the thread id 17101, but the former has a strange signature. Basically, I do not know what it does. The older thread 16543 looks very much the same as 17100, but whilst its associated query has successfully terminated, the thread 16543 lingers on. I have not yet found a reproducible procedure to create these zombie queries, but they do appear every now and then. Perhaps related, I have also noticed that not all MartView queries would necessarily generate an SQL query. In those cases, the little spinning and the text 'Loading...' would stay there forever. Since the marts of www.biomart.org seem to work perfectly well, I am wondering whether I am using old Perl code or an unpatched version of BioMart. Does anyone else experience these problems I am having? Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Enabling Count/Results buttons
Hello, I am now hijacking the 'Results' button for my purposes and eventually I would like to set some filters programmatically rather than through MartView. Even though Web.pm is rather complex, I think I have grasped the function of $session-param(...) now. Unfortunately, I am not quite sure how I would set a filter that way, since I do not know the exact parameters to the function. In order to get a deeper in-sight on what is going on, I tried to activate all the logging code which appears in the Perl module, but I have trouble finding the corresponding log-file. I grepped for 'Showing in browser' -- a phrase that should be in the log-file -- without any luck. I suspect that I have not really turned logging on. Is logging being activated by setting 'mode' and 'log_query' to ON in settings.conf? Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Enabling Count/Results buttons
2010/1/14 Junjun Zhang junjun.zh...@oicr.on.ca: Please make sure you have the following two lines in the conf/log4perl.conf file: Of course! Thanks a lot! However, as soon as I enable logging I get an 'Internal Server Error'. Luckily, I figured out how to set the parameters for $session-param(...) by a combination of reading Web.pm and trial and error now. Thanks a lot nevertheless, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Enabling Count/Results buttons
Hello, I am having trouble finding the code that enables/disables the 'Count' and 'Result' buttons in MartView. I assume it is somewhere hidden in either Web.pm or perhaps in the .tt template files, but I am not sure what to look for. Basically, I would like to enable my own form elements that I have added to the interface, as soon as the user has chosen a dataset. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Enabling Count/Results buttons
2010/1/13 Syed Haider syed.hai...@oicr.on.ca:
biomart-perl/conf/templates/default/menupanel.tt
I had a look at that file, which is also the place where I inserted my
own form elements. Whilst I can see that the buttons check 'onclick'
whether there is a dataset available, I cannot see where the buttons
are activated though. By the latter I mean un-greyed-out, i.e. made
click-able.
As a side note, I have to admit that the function of handle_request in
Web.pm is not quite clear to me. It seems to get called when I click
my 'submit' button, but only when the user has freshly selected a
dataset. Once the user has run any other query and pressed 'Results',
it appears to me that the code which I have put right before the line
'my $returnaAfterSave = 0;' in handle_request of Web.pm is not called
anymore. I find that strange, since I only surround my code with a 'if
($CGI-Vars()-{'myButton'})'. Is handle_request not called anymore
after a query is made?
Sorry for asking these programming questions -- especially as the code
will be obsolete soon -- but I am sure that there is a simple and
straightforward solution to my questions that I am just not being able
to see.
Thanks,
Joachim
--
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom
Re: [mart-dev] update a mart
Hello Kiran, 2010/1/7 Kiran Mukhyala mukhyala.ki...@gene.com: One problem I have right now is that in MartView, I don't see the Microarray section in the Feature Attributes page under the External attributes group. I do see the microarray attributes in MartEditor when I import from my local mart. We have the same problem, but we ignored it for now since we do not focus on that data in particular. It would be great if this issue could be resolved, because so far I always assumed that uploading the meta-data into the custom-build mart should be sufficient. BW, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] update a mart
2009/12/17 Kiran Mukhyala mukhyala.ki...@gene.com: In that case, I think I will need the MartBuilder XML files to create Ensembl-56 marts from scratch. I just asked for these files on ensembl-dev but please let me know in case you know where to find them. Have a look at: http://bergman-lab.blogspot.com/search/label/biomart I described there how to add custom data to the existing marts and I also provided XML-files for the Ensembl Mart 55. Unless you do something fancy, you can probably use the 55 XMLs and then run 'Update All Schemas' from the MartBuilder menu to let it pick up any changes. You have to do that step anyway to incorporate your custom data. If I remember correctly, either MartBuilder or MartEditor will come up with some error messages. Those are fine though. I can find out the exact messages and their cause once I am back from my holidays in two weeks. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Tool's Java Sources
2009/12/1 Syed Haider syed.hai...@oicr.on.ca: We will allow all developers plenty of time to play with the new system. Additionally, it will remain backward compatible. Just as a matter of interest: will the new system also make changes to the web-site templates (.tt files) and Perl modules? Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Tool's Java Sources
2009/12/7 Syed Haider syed.hai...@oicr.on.ca: Yes, the new system will replace the whole perl side of the project with Java. May I then suggest two improvements to the tabular display in MartView, which I have implemented in the soon-to-be obsolete Perl code: 1. alternate the background colour when the contents of the first column change, and 2. introduce a new data format that allows one to have tooltip-style pop-ups over link-out data. The first suggestion addresses the readability of MartView's output. Especially for larger tables with lots of columns and rows it is sometimes difficult to see where, for example, the data concerning one gene ends and the data for the next gene starts. By alternating colours, one gets a simple but effective visual grouping. The second suggestion is a bit esoteric, but I imagine that it could be useful for other people and projects too. I use it to display additional information about data that we incorporated into our BioMart. Displaying all of the data in the table would be too much, but if a user is interested about a particular entry in the table, then they can just hover the mouse over the respective item and see some supplementary information in the pop-up, before they finally decide whether they want, or do not want, to follow the link in question. As I have implemented it, the data is stored in the format 'x|y', where x is displayed in the table as a link and y is the HTML-formatted text that is displayed in the pop-up. Perhaps at least one of these suggestions sounds useful to the BioMart developers too.. :) Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Tool's Java Sources
Hello,
I have checked out the Java sources of release 0.7 and I am surprised
to see that there are so many warnings raised by Eclipse for them.
For example, in MartShellLib.java, lines 362-364 read:
//String handler = filter.getHandler();
String handler = null;
if (handler.equals(IDListFilter.FILE)) {
Surely, this is a genuine mistake. Eclipse also reports many unused
variables, i.e. assignments to variables which are never read.
Besides that, there are peculiar catch-cases, for example, in
MartEditor in uploadAll() there are two instances of:
} catch (Exception e) {
e.printStackTrace();
}
Should there not be a dialog for that as it is the case of
ConfigurationException-s in the very same method?
I also found that org.ensembl.util.StringUtil is missing from the CVS
repository, whilst it is present in the JAR-file of the mart tools.
The class is used by org.ensembl.mart.lib.Query and
org.ensembl.mart.util.StringUtil.
Since the code from the CVS repository does not compile, I assume
there is an inofficial official-repository for the source code
somewhere? Would it be possible to bring the source code of the 0.7
release up to speed, so that it represents the code actually used to
build the mart tools?
Thanks and Best Wishes,
Joachim
--
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom
Re: [mart-dev] Tool's Java Sources
Hello, 2009/12/1 Syed Haider syed.hai...@oicr.on.ca: over 75% of the code will be replaced, there wont be much there that you could reuse. Unfortunately, the preview is not available at this stage. But will do become in ~2-3 months time. Will that be a release for developers and testers, or will it rather be a stable release of new versions of MartBuilder, MartEditor, etc? I imagine rewriting more than three quarters of the 120,000+ lines of Java code in less than a year is fairly demanding (I assume the project started after the last 0.7 release). Even though it is a bit unorthodox, may I suggest that the new development repository might be opened to mart enthusiasts? There could be an appropriate disclaimer associated with the repository, so that it is clear that the sources are still undergoing rapid development. However, at least it would be able to get an overall impression in which direction BioMart is heading. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] HTML output in MartService
Hello Junjun, 2009/10/26 Junjun Zhang junjun.zh...@oicr.on.ca: We are looking into the problems and will get you back soon. Actually, I think the URL-linkout in MartView where you get links like http://.../martview/?VIRTUALSCHEMANAME=defaultATTRIBUTES=... seems to be doing pretty much the same job for me. I guess the output from MartView is more for programmatic processing anyway, so perhaps there is no need to investigate this further. Thanks for replying though, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] HTML output in MartService
Hello! I am using MartService to output the result of query, but instead of TSV I am outputting HTML. The query is http://www.biomart.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%3C!DOCTYPE%20Query%3E%3CQuery%20%20virtualSchemaName%20=%20%22default%22%20formatter%20=%20%22HTML%22%20header%20=%20%221%22%20uniqueRows%20=%20%220%22%20count%20=%20%22%22%20datasetConfigVersion%20=%20%220.7%22%20%3E%3CDataset%20name%20=%20%22hsapiens_gene_ensembl%22%20interface%20=%20%22default%22%20%3E%3CFilter%20name%20=%20%22chromosome_name%22%20value%20=%20%22Y%22/%3E%3CFilter%20name%20=%20%22ensembl_gene_id%22%20value%20=%20%22ENSG0234830%22/%3E%3CAttribute%20name%20=%20%22ensembl_gene_id%22%20/%3E%3CAttribute%20name%20=%20%22ensembl_transcript_id%22%20/%3E%3C/Dataset%3E%3C/Query%3E Unfortunately, my browsers (Firefox and Safari) render the output as plain text. Is there a tweak to make the browsers interpret the result as HTML? On an unrelated note, has someone experience with displaying formatted data in the pop-ups in the Ensembl Genome Browser from exported attributes using BioMart's DAS server? For example, when clicking on the Ensembl/Havana genes in the region view, I get a pop up telling me the gene ID/transcript ID with corresponding link-outs. Is it possible to do something like this using BioMart/DAS? BW, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Features visible in MartEditor, but they are not displayed in the web-interface
Hello! I have added some custom tables to the functional_genomics_mart_55 and changed the mart's meta-information in MartEditor accordingly. While this worked beforehand when I modified VEGA marts and Ensembl marts, the attributes/filters regarding my extra data are not displayed in the web-interface. However, when I import/export the functional_genomics_mart_55 annotated_feature dataset, I can clearly see my extra data. Is there an easy explanation to this? Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Features visible in MartEditor, but they are not displayed in the web-interface
Hello Syed, First of all, I mean of course annotated_feature template config in my previous post. 2009/9/7 Syed Haider s...@ebi.ac.uk: could you please write a details on which tables you have added, names please ? I have added a table 'mscript_ann_fea_blast_cdna' table to the various species, which links to the annotated features by its column 'annotated_feature_id'. I then run MartBuilder, update all schemas, build execute the SQL. There is plenty of data in the human and mouse mart-tables, but the fruit-fly's table dmelangoaster_regulatory_feature__mscript_ref_fea_blast_cdna__dm is empty. what did you do to add this info in MartEditor? please write the series of steps. In MartEditor I import the meta-info from martdb.ensembl.org and export it to my mart, then do the following: 1. connect to my mart 2. run 'Update All' 3. 'Import' where I choose annotated_feature 4. have a look at the attributes to see if there is a new collection with new attributes 5. 'Export' Then I run 'perl bin/configure.pl --clean -r conf/myMart.xml'. It is peculiar that the web-interface will not change even when I edit entries in MartEditor which are displayed in the browser. I wonder where the data comes from.. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Creating a single dataset for multiple species
Hello! 2009/8/13 Junjun Zhang junjun.zh...@oicr.on.ca: Thanks Richard. Yes, please try this first. If leaving includeDatasets empty in the registry doesn't help, please send me the xml files. The includeDatasets is empty, but perhaps the following output from 'perl bin/configure.pl ...' makes more sense to you: ... [NEW CONFIGURATION] WITH MEMORY [default] default ... My Mart 55 (unstable) ... 001/004 ... btaurus_my_ensembl (RDBMS) 127.0.0.1:1187 OK default ... My Mart 55 (unstable) ... 002/004 ... mmusculus_my_ensembl .. (RDBMS) 127.0.0.1:1187 OK default ... My Mart 55 (unstable) ... 003/004 ... celegans_my_ensembl ... (RDBMS) 127.0.0.1:1187 OK default ... My Mart 55 (unstable) ... 004/004 ... hsapiens_my_ensembl ... (RDBMS) 127.0.0.1:1187 OK default ... Vega Mart 54 (stable) 001/002 ... hsapiens_gene_vega (RDBMS) 127.0.0.1:1188 OK default ... Vega Mart 54 (stable) 002/002 ... mmusculus_gene_vega ... (RDBMS) 127.0.0.1:1188 OK ... Compiling templates for visible datasets [1/3] Attribute Panel of Dataset.. :hsapiens_my_ensembl [1/3] Filter Panel of Dataset. :hsapiens_my_ensembl [2/3] Attribute Panel of Dataset.. :hsapiens_gene_vega [2/3] Filter Panel of Dataset. :hsapiens_gene_vega [3/3] Attribute Panel of Dataset.. :mmusculus_gene_vega [3/3] Filter Panel of Dataset. :mmusculus_gene_vega I am puzzled that the script detects the datasets of the various species above, but then compiles the templates only for humans. Perhaps this is how it should be, but I am not sure. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Creating a single dataset for multiple species
Hello, 2009/7/20 Junjun Zhang junjun.zh...@oicr.on.ca: As Syed pointed out earlier on, you start with one species by run Naïve and Export the naïve configure to the database, and then Alt-N to bring in the other species. When prompted with the question Create new template rather than use existing one?, ask No. After this, a template configure will be created. When you expend the PartitionTable: Datasets node in the left tree panel, you should be able to see two Partition, one for each species. Don't forget to do Export again. From now on, you should be able to make changes to the configuration, and the changes will be propagate to the two species. Follow the same process to add more species as you need. Adding the species worked fine and I do indeed see several datasets in the tree on the left-hand side in MartEditor now. However, after exporting and running 'perl bin/configure.pl --clean -r conf/myMart.xml' again, I do not see the added species in the selection box '- CHOOSE DATASET -' in the BioMart web-interface. The selection box only contains the choice 'my ensembl', which corresponds to the name that I have chosen for the template in MartEditor. In fact, when I choose this entry, the data I can query seems to correspond to the first species for which I have run 'Naive' in MartEditor first. How do I make the other species appear in that selection box as well? Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Creating a single dataset for multiple species
Hello,
2009/7/20 Junjun Zhang junjun.zh...@oicr.on.ca:
It's not entirely clear what you wish to achieve, but I am under the
impression
that you want to merge 'hsapiens_gene_vega' and 'mmusculus_gene_vega' into
one dataset. If this is the case, you can not do it by changing configuration
in
MartEditor, the two datasets ('hsapiens_gene_vega' and 'mmusculus_gene_vega')
have to be physically merged, which should be fairly easy to do. Let us know
if
you need help with that.
Yes, I would like to merge the datasets. I would like to see one
single 'gene_vega' dataset, just as it is the case for the Vega mart
on martdb.ensembl.org, so that I will see the changes for both species
when I change my filter/attribute settings in that unified dataset.
How do I do that? Do I need to edit the XML-files representing the datasets?
Thanks,
Joachim
--
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom
[mart-dev] Creating a single dataset for multiple species
Hello! How do I create my own dataset (for example for the Vega Mart) in MartEditor? As it says in the documentation, I use the 'Naive' menu item to construct the rudimentary entries, but the first dialog-box only lets me choose a dataset per species. For example, the Vega Mart dataset is represented as 'hsapiens_gene_vega' and 'mmusculus_gene_vega', which is different to the single dataset 'gene_vega' of the Vega Mart on martdb.ensembl.org. I would like to have a single entry for my dataset regardless of the species as well, but I do not know how to do this in MartEditor. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Adding a filter to 'ID list limit'
Hello Syed, 2009/4/17 Syed Haider s...@ebi.ac.uk: Just wondering if you have declared the attribute which reflect the same filter in Attributes section. Please declare the attribute just like you did for the new filter (following same naming convention). That solved the problem. Just out of interest: why do the names of the filter and attribute have to coincide? I thought that the information in the filter is enough to perform a query. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Using MartView on vega mart with additional tables
Hello, I am struggling to get the web-interface MartView to display interesting data for an extended vega mart. The extended vega mart is build from the homo sapiens vega schema with an additional table 'gene_test' that has two columns 'gene_id' and 'annotation'. During the mart building process (with MartBuilder), I can see in the dataset view that the key of the new table is correctly associated with the gene table. I have then created the mart and after updating the meta tables using MartEditor I got an additional choice 'NEW_ATTRIBUTES' besides 'Features', Sequences' and 'Structures' for constructing queries in MartView and MartExplorer. In MartEditor I then dragged and dropped the 'AttributeGroup: new_attributes' so that it now appears under 'AttributePage: feature_page'. I ran the mart configuration again (perl bin/configure.pl ...) and now I can select 'Annotation 1077' besides other entries (e.g. 'VEGA Gene ID') in the 'Feature' panel. When I use MartExplorer, everything works fine, so that I can query the mart and get results accordingly. However, in MartView I can select the same checkboxes as in MartExplorer, but I get the following output: Validation Error: Attributes from multiple attribute pages are not allowed. Does anyone know what steps need to be undertaken in order to get the same query results in MartView as I get in MartExplorer? Is it not possible to arbitrarily move AttributeGroups and AttributeCollections around in MartEditor? Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
Re: [mart-dev] Using MartView on vega mart with additional tables
Hello Junjun, 2009/4/8 Junjun Zhang junjun.zh...@oicr.on.ca: If you were running configure.pl without --clean option, please make sure you do so, this may help solve the problem. This solved the problem! Thank you very much.. Best Wishes, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
[mart-dev] Building a mart, preferably fully automated
Hello, I am struggling with building a mart that resembles the ensembl_mart_52 (or any other version). I managed to set up simple marts myself, where I relied on BioMart's good documentation. However, it is not clear to me how I would set up bigger and more complex marts. Can anyone suggest a good tutorial for setting up my own version of ensembl_mart_52? Also, is there a way to automate the process of mart creation? Unless it is trivial to set up ensembl_mart_52, I would rather rely on a set of scripts or similar to repeat the mart building process for the Ensembl version 53 database. Thanks, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom
