Chado Controller User Manual
Contents
1. Your administrator may hide tracks to anonymous users using GBrowse config Unfortunately for technical reasons when you log in GBrowse needs to process the config to know how to authenticate you At the time it reads the config you are not authenticated yet and the tracks to be hidden to anonymous users remain hidden to you Then the page loads and you become authenticated You have to reload the page in order to let GBrowse reload its config and display the hidden tracks 3 Some checks made by the Annotation Inspector are not relevant Can I disable them To disable some checks made by the Annotation Inspector you have to ask your administrator to do so The Annotation Inspector calls functions that can be disabled by the administrator through the table annotation_inspector_procedures Note that checks can not be disabled for a specific user any change will be applied to all users 13 Chado Controller User Manual v1 0 0 Contacts valentin guignon O cirad fr stephanie sidibe bocs O cirad fr 14 Chado Controller User Manual v1 0 0 Glossary Annotation History it is a module of the Chado Controller package which records every modification made on data It is composed of PostgreSQL scripts embedded in the database and some parts of interface in GBrowse to display the annotation history The annotation history module is based on a modified version of the Chado Audit module to extend its initial possibilities Ann2. set to IC6 No significant functionnal prediction short coding sequence and or low coding probability product is doubtful protein Check consistency of evidence_code set to IC7 Very partial match and strong anomalies of the gene structure product is remant gene symbol Default behavior Commit beha report missing or invalid evidence_code CV term same behavior report missing product GO terms CV terms or Dbxref PMID report missing product GO terms CV terms or Dbxref PMID report missing product or GO terms CV terms report unwanted gene synonym CV term warn if product does not contain putative keyword report missing GO terms report unwanted gene synonym or ec number CV terms warn if product does not contain conserved hypothetical protein keywords warn if there is not just one GO terms set to molecular function report unwanted gene synonym or ec number CV terms warn if product does not contain hypothetical protein keywords warn if there is not just one GO terms set to molecular function warn if there are Dbxref PMID report unwanted gene synonym or ec number CV terms warn if product does not contain hypothetical protein keywords warn if there is not just one GO terms set to molecular function warn if there are Dbxref PMID report unwanted gene synonym or ec number CV terms warn if there is not just one product warn if the product contains h
3. Chado Controller User Manual Chado Controller User Manual v1 0 0 The Chado Controller package and all associated files are copyright c 2008 CIRAD Montpellier France The Chado Controller package is distributed under the Artistic License 2 0 Chado Controller User Manual v1 0 0 Preface The Chado Controller is a middleware that wraps a Chado Database to improve its possibilities It enables access restriction to Chado data verifies annotator work and keeps track of modifications made to the database This user manual targets annotators that use Artemis genome editor but also people using GBrowse genome browser It describes how the Chado Controller is integrated to these tools and how to take advantage of it Chado Controller User Manual v1 0 0 Table of content Chado Controller User anual casa iaa 1 A RETO AE isis 3 Table GE content asse TA AA IA AA A DA hentai senda DC TEN ico e cana a a dae dad cepa dados 4 EEN e BADEN io coa ERA NADO AT OS 5 Access RESHICH ON Mol di 5 Logging in and logging QU siii train naaa aan 5 AMMO AMON Inspector dao dis 5 Annotation A AA AS 11 PPOUDIESHC OU NS dada doce 12 Frequently Asked Questions a n O e IR DEU Sa 13 COMAS TA TI A EA A PET AA A TA da Onda paes 14 SLOSS AI ese Sede E E A ESTE nae A 15 Chado Controller User Manual v1 0 0 Basics The Chado Controller is a middleware mainly embedded in a Chado Database It is composed of 3 main parts 1 the Access Restricti
4. ator uses the Commit button Then it performs its checks and either just commits if everything was fine or displays a dialog box reporting encountered issues When issues are detected the annotator can commit his her changes anyway or cancel to fix the problems If the Annotation Inspector is told to commit while issues were reported it will add properties to the annotated element indicating which issues were detected When using front end programs to PostgreSQL such as psql command line program the Annotation Inspector can be called manually To check the whole database for annotation issues you can use the SQL command SELECT FROM validate_annotations 0 FALSE To start a new manual annotation and check it for issues do the following queries SELECT start_new_transaction_group Then note the returned value which is the transaction group identifier that will be used later on START TRANSACTION Do your annotation SQL queries SELECT INSERT UPDATE DELETE Once done to check your work do SELECT FROM validate_annotations lt identifier gt FALSE where lt identifier gt is the transaction group identifier you got earlier That call will return 2 fields a filed validation which is set to O if no issue has been encountered and a field validation_message containing encountered issues description Then you have 3 choices you can just ignore the Annotation Inspector resu
5. check and manage procedures admin account includes both administrator and database loading accounts Function Annotation Inspector Rule Default behavior Auto owner Set owner to current user for new polypeptide or repeat region except when using admin handled by triggers account Set owner to current user on polypeptide or repeat region when a qualifier is added or modified handled by triggers except when using admin account Set owner to current user on polypeptide or repeat region when a gene element position ora CV handled by triggers term or a feature dbxref is added or modified except when using admin account Auto manual Curation Add any modified features to manual curation track feature_dbxref relationship handled by triggers Auto Color Set color of related features of gene or repeat region to the color choosen at Chado Controller handled by triggers installation time when a gene related or a repeat region related feature is modified Auto TE Relationship Insert missing feature_relationship entries between repeat region related features when any of handled by triggers them is modified Chado Controller User Manual v1 0 0 Function check_gene_structure Annotation Inspector Rule Check if the obsolete status of an element is consistent with its associated elements Default behavior for non obsolete gene report missing non obsolete mRNA report missing non obsolete polypeptide report missing non obsolete exon
6. found inside the coding sequence add multiple_stop_in_frame CV term if more than a stop c has been found inside the coding sequence remove stop in frame and multiple_stop_in_frame if no codon has been found inside coding sequence check_introns report negative intron length report unrecognized intron donor site non GT report unrecognized intron acceptor site non AG add negative_intron_length CV term when negative intron length detected add missing_donor CV term when an unrecognized intron donor site non GT is found add missing_acceptor CV term when an unrecognized int acceptor site non AG is found manage_evidence add curated CV term when a feature is modified same behavior manage_note auto set note qualifier content to something like name product gene completeness for genes or rpt_class rpt_order rpt_superfamily rpt_family name rpt_type completeness and fill mobile_element qualifier for repeat regions or satellite name and fill satellite qualifier for satellites same behavior manage transposable element gene add transposable_element_gene qualifier set to 1 for genes inside a repeat region or a transposon or if the gene has one of the detected keyword in its product qualifier or if the gene ha a detected IPR code as dbxref if the transposable_element_gene has already been set its value remains unchanged even if it is set to 0 same behavior manage_mandatory_p
7. is the relational database management system that handles Chado databases 15
8. lts and commit COMMIT you may want to commit but keep track of what was wrong SELECT FROM validate_annotations lt identifier gt TRUE COMMIT or cancel all your changes ROLLBACK To check an older annotation you need administrator access right to get the annotation transaction identifier of the annotation This identifier can be found in the audit tables Annotation History p 11 Typically a query to retrieve such an identifier looks like this SELECT transaction_group FROM lt table gt _audit WHERE lt come condition to identify the annotation gt GROUP BY transaction_group transaction_date ORDER BY transaction_date DESC For instance to retrieve annotations made on a feature between September the 1 and September the 2 SELECT transaction group FROM feature audit WHERE 2011 09 01 00 00 00 lt transaction date AND transaction date lt 2011 09 02 23 59 59 GROUP BY transaction group transaction date ORDER BY transaction date DESC The checks performed by a standard installation of the Annotation Inspector and its behavior when validate annotations is called with TRUE as second argument are listed in Table 1 Note each one of the above functions can be called the same way validate annotations is Table 1 Annotation rules of the Chado Controller manual annotation tracking module Functions called by the validate_annotations function auto fill triggers
9. make sure gene name is shared between gene elements report last stop codon shared between at least 2 different non obsolete genes for obsolete gene report non obsolete mRNA report non obsolete polypeptide report non obsolete exon for deleted gene report non deleted mRNA report non deleted polypeptide report non deleted exon for non obsolete mRNA report missing non obsolete gene report missing non obsolete polypeptide report missing non obsolete exon for obsolete mRNA report non obsolete gene report non obsolete polypeptide report non obsolete exon for deleted mRNA report non deleted gene report non deleted polypeptide report non deleted exon Commit behavi add redundant gene if a stop codon is share between at least 2 gen otherwise remove redundant_gene quali Chado Controller User Manual v1 0 0 Function Default behavior Commit behavior check start stop codons report invalid start or stop codon add missing start codon CV term for invalid start codon add missing_stop_codon CV term for invalid stop codon check_sequence report sequence length which are not a multiple of 3 add not_3 multiple CV term if sequence length is not a mt add peptide CV term if polypeptide lenght is below 60bp report any stop codon found inside the coding sequence of 3 add peptide CV term if polypeptide lenght is below 60bp add stop in frame CV term if only one stop codon has be
10. on editor Chado Controller User Manual v1 0 0 Troubleshooting 1 I can t log in Make sure you use the appropriate login and password and Caps Lock on your keyboard is not turned on If you are really sure your password is correct see with your administrator He she can have access to log files that could provide additional information on the source of the problem 2 I can login with GBrowse but not with Artemis The Chado Controller can not use PostgreSQL account passwords to authenticate users Therefore it is possible that the password of the Chado account is desynchronized with the password of the PostgreSQL account If you change your password using the GBrowse interface it might help to resynchronize your passwords If the problem remains see with your administrator 3 I can t access to the tracks I m supposed to First make sure you are logged in using the appropriate account Then make sure your administrator granted you the appropriate rights on the tracks 12 Chado Controller User Manual v1 0 0 Frequently Asked Questions 1 How do I know if I m logged in using a specific login On GBrowse the Access Restriction module adds a small area box entitled User Account In that area if you re logged in there will be a button starting with Logout followed by the name of the user account you are currently using 2 Why do I have to reload GBrowse page after login to see all protected tracks
11. on module 2 the Annotation Inspector 3 the Annotation History module Access Restriction Module The Access Restriction module manages the access to any feature of the database chromosome contig gene mRNA protein regions Logging in and logging out When using GBrowse users may have to login in order to access to protected features To log in there should be a box on the top of GBrowse labelled User Account with 2 fields Login and Password Simply enter your login and password and click on the button Login The page should be reloaded and a display the message Welcome lt your login gt if you logged in successfully Once logged in you can change your password using the link Change password which displays two fields one for the new password and a second one to type the new password again to ensure there are no mistyping Then the change password button will proceed to the password update Be careful after login you have to have to update image in the GBrowse page to see all protected tracks Frequently Asked Questions p 13 With Artemis the user just has to log into the Chado database using the regular Artemis login box and the Access Restriction module will manage his her access rights automatically New created feature will be given the same access right of the object they are located on ie through Chado featureloc table When using front end programs to PostgreSQL s
12. ory musa name MaC088K20_ 300 Login guest password guest GBrowse history page can display 2 kinds of reports one for gene or polypeptides features and one for other kinds of features For genes only the history of the following properties will be displayed while the history of other properties is also in database e Feature fields feature table locus_tag name length seqlen e Feature properties featureprop table owner note inference annotator_comment e Feature controlled vocabulary terms feature_cvtem table product functional completeness gene EC_number e Feature database cross references feature_dbxref table PMID For other features displayed properties are owner note comment annotator_comment inference length Functional Completeness Evidence Code Gene locus_tag and PMID Note only the available properties will be displayed The annotation history page displays group of transactions in colored blocks with the date and the author of the changes for each group of transaction Group of transaction are stored by date the most recent being the first block displayed Properties that have been changed during a transaction group are displayed in bold When multiple changes occur on a same property a plus sign is displayed to show all the changes made Currently it is not possible to restore an old annotation If you want to do so you will have to copy the old annotation and paste it on your annotati
13. otation Inspector it is a module of the Chado Controller which automates some annotation tasks and can be used to check the consistency of annotations It is composed of PostgreSQL scripts embedded in the database and some parts of interface in Artemis to display inspector messages It is based on controlled vocabularies CV Access Restriction it is a module of the Chado Controller which enables access control to features of a Chado Database It is composed of PostgreSQL scripts embedded in the database and some parts of interface in GBrowse or Artemis for initialisation of the module or user login Chado Chado is a relational database schema that underlies many GMOD installations It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence sequence comparisons phenotypes genotypes ontologies publications and phylogeny Chado Controller it is a middleware between a Chado database and user interfaces that use it It is composed of 3 main modules Access Restriction module Annotation Inspector module and Annotation History module Controlled Vocabulary a controlled vocabulary is a list of terms grouped under a vocabulary name It helps the annotator to find the allowed terms and prevents the creation of duplicate terms often due to typo e g product gene symbol EC number functional completeness structural completeness status evidence evidence code PostgreSQL it
14. roperties report missing product qualifier report missing functional_completeness qualifier report missing status qualifier report missing evidence qualifier report missing or not set inference qualifier same behavior Chado Controller User Manual v1 0 0 Function manage_evi dence_code _coherence Annotation Inspector Rule Report inconsistency between gene qualifiers and the selected evidence code Check consistency of evidence_code set to IC1 Similarity with a polypeptide whose function has been experimentally demonstrated in the studied organism OR in the same genus product is the validated function of the cognate polypeptide Check consistency of evidence_code set to IC2 or IC2a High similarity with a polypeptide of validated function product is the validated function of the ortholog Check consistency of evidence_code set to IC2b High similarity with a polypeptide of known function product is the known function of the ortholog Check consistency of evidence_code set to IC3 Similarity with Swissprot TrEMBL polypeptide or InterPro family product is the putative function of the homolog Check consistency of evidence code set to IC4 Similarity with polypeptide of unknown function or interspecies EST product is conserved hypothetical protein Check consistency of evidence_code set to IC5 No significant blast hit product is hypothetical protein Check consistency of evidence_code
15. uch as psql command line program you should manually initialize the Access Restriction module using the SQL command SELECT init_access If you don t do so your first query using the feature table will be slower than expected as the Access Restriction module will proceed to a self initialization and treat your query in a non optimized way Annotation Inspector The Annotation Inspector helps annotators to produce consistent annotations It is based on controlled vocabularies CV CV owned by the Chado Controller are prefixed by CC The CC cvterms are available through the CV tab of Artemis feature builder or at http www gnpannot org sites gnpannot org files chado_controller_1 6 0 tgz The Annotation Inspector automates some annotation tasks so the annotator doesn t have to handle these anymore such as add new feature to the manual annotation track update feature_dbxref source as source and type are required by GBrowse change the color feature property of annotated features according to their annotation status colours are selected by the administrator at installation time Chado Controller User Manual v1 0 0 set the owner property of a gene to current user add relationship entries between sub elements of a transposable element The Annotation Inspector can also be called to check the consistency of an annotation When integrated to Artemis the Annotation Inspector is automatically called when the annot
16. ypothetical or putative keywords warn if there is not just one GO terms set to molecular function warn if there are Dbxref PMID 10 Annotation History The Annotation History module keeps track of every insertion update or deletion made on Chado tables Annotation history includes the login of the user who performed the changes and the date of the operation Moreover changes are grouped into transaction groups and their order is recorded When a transaction group identifier is positive it means changes were made without calling the function start_new_transaction_group On the opposite if the identifier is negative it means that start_new_transaction_group has been called So you can easily differentiate what was done with a Chado Controller compliant soft such as Artemis The history of a gene or a transposable element can be accessed from GBrowse using the script http lt your GBrowse site gt cgi bin gbrowse_history lt your Chado instance gt name lt your gene gt Where lt your GBrowse site gt is the name of the server hosting your GBrowse lt your Chado instance gt is the name of the Chado instance you use and lt your gene gt is the name of the gene of interest Note you can also get the URL of the history page of a feature by replacing obrowse details with gbrowse history if you have the GBrowse details page URL Example http gnpannot cirad fr cgi bin gbrowse_hist
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