[base] tab2mage/annotation questions
Hi, We're making a concerted effort to move operations to BASE 2 now... I have been reading up on annotating experiments in preparation for future tab2mage export: http://base.thep.lu.se/chrome/site/doc/html/userdoc/analysis/experiments_analysis.experiments.html#experiments_analysis.magexport Dumb question: An Annotation Type such as Age(hours) or body mass(kg) when applied to a biosource will be exported as a BioMaterialCharacteristic, right? We don't have to mark/tag the Annotation Type as a 'BioMaterialCharacteristic' in some way? I guess it would be good to put all of these in an Annotation Type Category (called BioMaterialCharacteristic, for example), but that's just for convenience? And a related question: we (base admins) should create Annotation Types just for the 'leaves' in the MGED ontology, is that correct? Is there a convention for capitalisation, spaces etc? e.g. 1. DevelopmentalStage 2. Developmental Stage 3. developmental stage It's not consistent in the manual (see link above) e.g. Age(week) - capitalised body mass(kg) - lower case body temperature (degree_C) - an extra space before the units Has anyone made any progress importing MGED or other ontologies as a whole? While we're at it, a more advanced question: say we have a Biosource Annotation Type called OrganismPart, which is free text (or a text enum). How could you enter values from a separate anatomy ontology, so that it goes into tab2mage correctly (or perhaps MAGE-TAB at a later date)? Thanks for reading this far! cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] tab2mage/annotation questions
Hi Bob http://base.thep.lu.se/chrome/site/doc/html/userdoc/analysis/experiments_analysis.experiments.html#experiments_analysis.magexport Dumb question: An Annotation Type such as Age(hours) or body mass(kg) when applied to a biosource will be exported as a BioMaterialCharacteristic, right? We don't have to mark/tag the Annotation Type as a 'BioMaterialCharacteristic' in some way? I guess it would be good to put all of these in an Annotation Type Category (called BioMaterialCharacteristic, for example), but that's just for convenience? You would not need a new category for BioMaterialCharacteristic, I reckon biosource annotations should simply be exported as a BioMaterialCharacteristic. And a related question: we (base admins) should create Annotation Types just for the 'leaves' in the MGED ontology, is that correct? Is there a convention for capitalisation, spaces etc? e.g. 1. DevelopmentalStage 2. Developmental Stage 3. developmental stage It's not consistent in the manual (see link above) e.g. Age(week) - capitalised body mass(kg) - lower case body temperature (degree_C) - an extra space before the units Has anyone made any progress importing MGED or other ontologies as a whole? I haven't made any effort at importing MGED ontologies and I do not know of any convention for capitalisation in Base2. While we're at it, a more advanced question: say we have a Biosource Annotation Type called OrganismPart, which is free text (or a text enum). How could you enter values from a separate anatomy ontology, so that it goes into tab2mage correctly (or perhaps MAGE-TAB at a later date)? I don't understand this fully. Do you mean into base2 first and then exported in tab2mage? Also, we have a tab2mage export available on the base2 plugin source code (svn) page. Its not been packaged as a separate plugin distribution yet. However, we are hoping to do this soon. It need some extra enhancements. -- ¬Dominic - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] affymetrix
Hello, Just a couple of things regarding using Affymetrix with BASE. i. We are just about to release a plugin to create ArrayDesigns from a bunch of zipped CDF files. This should speed up part of the process of managing Affymetrix Designs. Will post when ready. ii. I have a little simple perl script that connects to Affymetrix web site and retrieves the annotations files, converts those from csv to tab delimited so they are ready to be used for importing Reporters in conjonction with the Affymetrix Reporter Importer Plugin configuration. I have had pb using the csv file from Affymetrix as there are 'comma' used as separator within a field. Depending on how much one wants to store of the Affymetrix annotations, the extended-properties.xml file may have to be modified, and the database upgraded before running the plugin. If not, then those files can used to load ProbeSet ID (email me offline for the script). For the moment, sorry folks, no plugin for batch importing the reporters from a bunch of annotation files iii. For information only, I have managed to configure and run RMAExpress and PLIER plugin on windows machine. Have to add to the documentation. cheers Philippe Bob MacCallum wrote: Emmanuel Courcelle wrote: Hello Trying to use BASE with affymetrix data. me too! 2/ I can't see any new Reporter in the View/Reporters You need to import the reporter from a reporter annotation file (.csv). See http://lev.thep.lu.se/trac/baseplugins/browser/tags/se/lu/thep/affymetrix-0.6/README for details. could someone point me to these .csv files please? I've downloaded the xxx_libraryfile.zip (containing a .cdf file amongst others) but no .csv file. Do you get this from NetAffx online? many thanks, Bob. -- Philippe Rocca-Serra (Ph.D) NET Project - Technical Coordinator http://www.ebi.ac.uk/net-project EBI- The European Bioinformatics Institute EMBL Outstation Hinxton Wellcome Trust Genome Campus CB10 1SD Cambridge, UK email: [EMAIL PROTECTED] Tel: +44 (0) 1223 492 553 Fax: +44 (0) 1223 494 468 European Nutrigenomics Organization http://www.nugo.org - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] tab2mage/annotation questions
Hello Bob, Dumb question: An Annotation Type such as Age(hours) or body mass(kg) when applied to a biosource will be exported as a BioMaterialCharacteristic, right? Yes, they will. Also an important point: since tab2mage specifications only allow for BioMaterialCharacteristics to be attached to BioSources, all annotations attached to items other than BioSource are not exported. This issue will be solved when implementing the MAGE-TAB specifications which are more flexible. We don't have to mark/tag the Annotation Type as a 'BioMaterialCharacteristic' in some way? I guess it would be good to put all of these in an Annotation Type Category (called BioMaterialCharacteristic, for example), but that's just for convenience? AnnotationType can be marked as Parameter (which then excludes them to be used as BiomaterialCharacteristics). In that respect, the default assumption is that if AnnotationTypes are used to annotate Biomaterials then they are considered as BioMaterialCharacteristics. And a related question: we (base admins) should create Annotation Types just for the 'leaves' in the MGED ontology, is that correct? Is there a convention for capitalisation, spaces etc? e.g. 1. DevelopmentalStage 2. Developmental Stage 3. developmental stage Thanks for pointing this out, I will fix this. To be compliant with tab2mage parser, case1 is the valid one (MGED ontology use CamelCase convention for its classes.) the list of valid 'leaves' is available here: http://mged.sourceforge.net/ontologies/MGEDontology.php#BioMaterialCharacteristics It's not consistent in the manual (see link above) e.g. Age(week) - capitalised body mass(kg) - lower case body temperature (degree_C) - an extra space before the units The tab2mage specs are clearer when it comes to declaration of parameters. Please see http://tab2mage.sourceforge.net/docs/detail.html#protoparams And there are notes regarding declaration of FactorValue, here: /'FactorValues may be linked to either Values or Measurements/. As a rule of thumb, Tab2MAGE currently assumes that a purely numerical value in a FactorValue column should be encoded as a Measurement. In such situations the /category/ field should indicate the class and name of the measurement unit, in the form: FactorValue[unit class(unit name)] For example: FactorValue[Temperature(degree_C)] Again will fix the doc. Has anyone made any progress importing MGED or other ontologies as a whole? Not yet :( While we're at it, a more advanced question: say we have a Biosource Annotation Type called OrganismPart, which is free text (or a text enum). How could you enter values from a separate anatomy ontology, so that it goes into tab2mage correctly (or perhaps MAGE-TAB at a later date)? I am still exploring using several different sets of annotations that would be shared on specific projects to answer that use case. This could solve the problem of users being confronted with AnnotationTypes and values which are not relevant to them . But this does not solve the pb of mixing and matching within one Ontology Category. A work around would be some convention for specifying Source Ontology and value. Again this is suboptimal but might a necessary evil to be able to support MAGE-TAB specifications. Or more drastically, only stick to using OBO foundry ontologies and if terms are missing from those resources, contact the editors and submit the missing terms. All OBO foundry ontologies are very reactive and will advise for alternate terms. thanks for your input. Philippe Philippe Rocca-Serra (Ph.D) NET Project - Technical Coordinator http://www.ebi.ac.uk/net-project EBI- The European Bioinformatics Institute EMBL Outstation Hinxton Wellcome Trust Genome Campus CB10 1SD Cambridge, UK email: [EMAIL PROTECTED] Tel: +44 (0) 1223 492 553 Fax: +44 (0) 1223 494 468 European Nutrigenomics Organization http://www.nugo.org - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] affymetrix
Bob MacCallum wrote: Emmanuel Courcelle wrote: Hello Trying to use BASE with affymetrix data. me too! 2/ I can't see any new Reporter in the View/Reporters You need to import the reporter from a reporter annotation file (.csv). See http://lev.thep.lu.se/trac/baseplugins/browser/tags/se/lu/thep/affymetrix-0.6/README for details. could someone point me to these .csv files please? I've downloaded the xxx_libraryfile.zip (containing a .cdf file amongst others) but no .csv file. Do you get this from NetAffx online? Just for information. Base 2.4 will include a plug-in that can create reporters directly from a CDF file. The plug-in can only set the probeset ID since that is the only info that is available in the CDF. To get other annotation information you still need the .csv file(s). There will also be validation to make sure that CEL:s are matched with the proper CDF:s. These two things should make it easier and less error-prone to use Affymetrix data and the RMAExpress and Plier plug-ins. /Nicklas - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
