Home

CycADS User Manual

1. GBKLoader file debug outputGbkFile the name of the file to output the updated genbank file to after the editions GBKLoader file lt type gt featureSynonym tagName regex lt i gt GBKLoader file lt type gt featureSynonym tagValue rege x lt i gt and GBKLoader file lt type gt featureSynonym dbName lt i gt these parameters are used to assign synonyms to the SubseqFeatureAnnotation entity created with the feature information in the genbank file If a tag name and the tag value of this feature match with respectively GBKLoader file lt type gt featureSynonym tagName regex lt i gt and GBKLoader file lt type gt featureSynonym tagValue regex lt i gt then CycADS will create a synonym to the feature with the DBName equal to the argument GBK Loader file lt type gt featureSynonym dbName lt i gt and accession equal to the tag value GBKLoader file lt type gt featureParent tagName regex lt i gt GBKLoader file lt type gt featureParent tagValue regex lt i gt and GBKLoader file lt type gt featureParent dbName lt i gt these parameters are used to assign parents to the SubseqFeatureAnnotation entity created with the feature information in the genbank file If a tag name and the tag value of this feature match with respectively GBKLoader file lt type gt featureParent tagName regex lt i gt and GBKLoader file lt type gt featureParent tagValue regex lt i gt then CycADS will create the parents of the feature with the entities that
2. created The Dbxref and Synonym identifications are DBxRef If the DBxRef don t exist then the program will create one The line command is org cycads ui loader DbxrefSynonymLoader lt fileName gt lt sourceColumnIndex gt lt sourceDBName gt lt synonymColumnIndex gt lt synonymDBName gt where fileName name and path of the file to load sourceColumnIndex the number of the dbxref identifications column sourceDBName the external database name of the dbxref identifications This database name will be used if the dbxref identification doesn t have a database name synonymColumnIndex the number of the Synonym column synonymDBName the external database name of the Synonym This database name will be used if the Synonym identification doesn t have a database These parameters can be set in the config properties 3 2 Program to extract annotations to a file CycADS can export data in the Pathologic file format used by Biocyc databases Pathway Tools Data output can be filtered using the command line parameters and mostly using the configuration file config properties The command line CycADS has the following extractor programs org cycads ui extract cyc AnnotationGenerator lt fileName folderName gt lt organismNumber gt lt seqDbname seqAccession gt lt seqVersion gt lt sequenceLocation gt lt ecThreshold gt lt goThreshold gt lt fileFormat gt where fileName folderName name and path of the file to generate or path to th
3. cycads ui loader GBKLoader lt fileName gt lt seqDBName gt where fileName name and path of the Genbank file to load seqDBName database name of the sequence accession The sequence accession is located in the genbank file The DBxRef object created with the segDBName and accession will be stored in the database and will be the synonym of the sequence After these parameters the loader accepts many parameters by config properties to interpret the genbank file content and to transform it in the CycADS database format A lt type gt or feature config type name in the parameter name in the config properties means that the respective argument is applied only to features of the type lt type gt The parameters in the config file are GBKLoader file sequence dbName the same as the segDBName line command parameter GBKLoader file fileName the same as the fileName command line parameter GBKLoader file sequence description noteType the note type of the note entity to store the description or definition of the sequence indicated in the genbank file GBKLoader file sequence comment noteType the note type of the note entity to store the notes or comments of the sequence indicated in the genbank file GBKLoader file removeType regex lt i gt if the argument matches with the type name of a feature in the genbank file then this feature will be thrown out and will not be loaded GBKLoader file changeType regex lt i gt and GBKLoader file cha
4. feature name of the SubseqFeatureA nnotation object will be lt type gt GFF3Loader file lt type gt lt source gt methodName gives the annotation method name for the annotations of the type lt type gt and source lt source gt GFF3Loader file attribute lt type gt lt source gt removeTag regex lt i gt if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt removeTag regex lt i gt then this attribute will not be load by the program GFF3Loader file attribute lt type gt lt source gt replaceTagName regex lt i gt and GFF3Loader file attribute lt type gt lt source gt replaceNewTagName regex lt i gt if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt replaceTagName regex lt i gt then the tag name of this attribute will be changed to GFF3Loader file attribute lt type gt lt source gt replaceNewTagName regex lt i gt GFF3Loader file attribute lt type gt lt source gt annotationCompletSynonymTag regex and GFF3Loader file attribute lt type gt lt source gt annotationCompletSynonymSeparator if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt annotationCompletSynonymTag regex then the tag value of this attribute will be used to create a DBxRef as synonym of the SubseqFeatureAnnotation object The DBName a
5. have a synonym with DBName equal to GBK Loader file lt type gt featureParent dbName lt i gt and accession equal to the tag value GBKLoader file lt type gt subseqSynonym tagName regex lt i gt GBK Loader file lt type gt subseqSynonym tagV alue regex lt i gt and GBKLoader file lt type gt subseqSynonym dbName lt i gt these parameters are used to assign synonyms to the Subsequence entity of the SubseqFeatureAnnotation entity The parameters usage are similar to the SubseqFeatureAnnotation synonym creation GBKLoader file lt type gt subseqDbxRefA nnotation tagName regex lt i gt G BK Loader file lt type gt subseqDbxRefAnnota tion tagValue regex lt i gt GBKLoader file lt type gt subseqDbxRefAnnotation dbName lt i gt and GBKLoader file lt type gt subseqDbxRefAnnotation methodName lt i gt these parameters are used to create SubseqDbxRefAnnotation objects with the annotation method equal to GBK Loader file lt type gt subseqDbxRefAnnotation methodName lt i gt They are used with the feature information in the genbank file such that the subsequence is the subsequence of the SubseqFeatureAnnotation entity created the DBxRef is GBKLoader file lt type gt subseqDbxRefAnnotation dbName lt i gt lt tag value gt and the tag name and its tag value match with respectively GBK Loader file lt type gt subseqDbxRefAnnotation tagName regex lt i gt and GBKLoader file lt type gt subseqDbxRefAnnotation methodName lt i gt GBK
6. the number of the score column If there is not a value in the column indicate by this parameter then the annotation object will not have a score methodColumnIndex the number of the method column If there is not a value in the column indicate by this parameter then the method name of the annotation object will be the method name default indicated in the methodName parameter The parameters in the config properties are The same as above which will be used when they are missing in the command line parameters Note that confirmation is asked to the user with an input dialogbox Additional parameters about the file format can must be set such as column separator line comments chars and so on subseqDbxrefAnnotationLoader organismNumber the same as the organismNumber line command parameter subseqDbxrefAnnotationLoader fileName the same as the fileName command line parameter subseqDbxrefAnnotationLoader methodName the same as the methodName command line parameter subseqDbxrefAnnotationLoader subseqColumnIndex the number of the subsequences identification column subseqDbxrefAnnotationLoader subseqDBName the subsequence DB name subseqDbxrefAnnotationLoader dbxrefColumnIndex the number of the DBxRef column subseqDbxrefAnnotationLoader dbxrefDBName the DBxRef external DB name subseqDbxrefAnnotationLoader scoreColumnIndex the number of the score column subseqDbxrefAnnotationLoader methodColumnIndex the number of the score method column subse
7. the program and it will be not included in the list If there is only one argument in the list to pass to the program the number i 0 is optional e lt value gt corresponds to the argument passed to the program or the value assigned to the parameter The words enclosed by appears only in some parameters All arguments passed by the command line can be passed by the config properties but the command line arguments will overwrite the arguments of the same parameters passed in the config properties moreover these arguments in config properties will be used as default value in a question window to confirm the choice 3 1 Loader programs CycADS can import or load data from several sources and formats CycADS has the following loader programs GBKLoader Import data from GenBank Flat File Format http www ncbi nlm nih gov Sitemap samplerecord html A feature annotation CDS mRNA gene etc in the GenBank file is described with its location subsequence in the sequence and other informations e g name parent synonyms EC number etc presente as a list of tags We will say that one tag is composed of a tag name and in general a tag value This program can store in the database all types of entities except DBxRefDBxRefAnnotation Beyond the entities the program can create and store e synonyms for Sequences Subsequences and SubseqFeatureAnnotations and e enotes for Sequences and SubseqFeatureAnnotations The line command is org
8. this parameter then the method name of the annotation object will be the method name default indicated in the methodName parameter The parameters in the config properties are The same as above which will be used when they are missing in the command line parameters Note that confirmation is asked to the user with an input dialogbox Additional parameters about the file format can must be set such as column separator line comments chars and so on as shown in the previous SubseqDbxrefA nnotationLoader loader DbxrefDbxrefAnnotationLoader This program loads DbxrefDbxrefAnnotation objects created from a text file with columns delimited by a string The column delimiter string is given by one parameter in the config properties file The file must have at least 2 columns the dbxrefSource identifications column or dbxrefSource DBxRefs column and the dbxrefTarget identifications column Given a line in the file for each pair dbxrefSource dbxrefTarget identified one DbxrefDbxrefAnnotation object is created The dbxrefSource and the dbxrefTarget identifications are DBxRefs They will be created if not exist The line command is org cycads ui loader DbxrefDbxrefAnnotationLoader lt fileName gt lt methodName gt lt sourceColumnIndex gt lt sourceDBName gt lt targetColumnIndex gt lt targetDBName gt lt scoreColumnIndex gt lt optional methodColumnIndex gt where fileName name and path of the file to load methodName the default method
9. I 2 3 CycADS User Manual System overview The CycADS database The programs 3 1 Loader programs GBKLoader GFF3Loader KOLoader SubseqDbxrefAnnotationLoader EntityDbxrefAnnotationLoader DbxrefDbxrefAnnotationLoader EntitySynonymLoader DbxrefSynonymLoader 3 2 Program to extract annotations to a file The command line Config properties 3 3 Auxiliary programs Usage examples System requirements Installation Troubleshooting Future works ODODOOAONNUWWW N N CycADS is a system designed and developed to build a BioCyc database using many different annotation sources The system is on GNU License and can be downloaded freely including the source code from http code google com p cycads 1 System overview We made one very flexible system to import data from several different file formats into a database and to export data from the database to a file format pf file specifically required by the Pathologic program of the PathwayTools system This pf file can be generated with different filters and options The filters can be applied to the external reference links and to the annotations used by PathwayTools EC and GO numbers The system CycADS was developed in Java and therefore can be executed in many different operating systems see the section System requirements for details The system code can be split logically in 3 layers Data Classes and interfaces to access and represent the entities used in the sy
10. Loader file lt type gt subseqFunctionAnnotation tagName regex lt i gt G BKLoader file lt type gt subseqFunctionAnn otation tagValue regex lt i gt and GBKLoader file lt type gt subseqFunctionA nnotation methodName lt i gt these parameters are used to create SubseqFunctionAnnotation objects with the annotation method equal to GBKLoader file lt type gt subseqFunctionAnnotation methodName lt i gt They are used with the feature information in the genbank file such that the subsequence is the subsequence of the SubseqFeatureAnnotation entity created the Function name is the tag value and the tag name and its tag value match with respectively GBKLoader file lt type gt subseqDbxRefAnnotation tagName regex lt i gt and GBKLoader file lt type gt subseqDbxRefAnnotation methodName lt i gt GFF3Loader Import data from GFF3 File Format http www sequenceontology org gff3 shtml The GFF3 file is used to describe sequence feature annotations CDS mRNA gene etc This program loads CDS RNA and gene feature annotations SubseqFeatureAnnotation entities The exons are considered just to create the RNA introns and consequently the CDS introns The others features types are ignored by this program Each feature annotation in the GFF3 file is described in a line of 9 tab delimited columns There are columns to inform feature annotation type feature annotation location source sequence synonym start end and strand annotation metho
11. column or entity DBxRefs column and the DBxRef identifications column Given a line in the file for each pair Entity DBxRef identified one EntityDbxrefA nnotation object is created The entity identification or entity DBxRef is a DBxRef which must be an entity synonym If the entity DBxRef don t reach an entity by the entity synonym then the program will do nothing The line command is org cycads ui loader EntityDbxrefAnnotationLoader lt fileName gt lt methodName gt lt sourceColumnIndex gt lt sourceDBName gt lt targetColumnIndex gt lt targetDBName gt lt scoreColumnIndex gt lt optional methodColumnIndex gt where fileName name and path of the file to load methodName the default method name to be used to create the EntityDbxrefAnnotation object sourceColumnIndex the number of the entity identifications column sourceDBName the external database name of the entity identifications This database name will be used if the entity identification doesn t have a database name targetColumnIndex the number of the DBxRef column targetDBName the external database name of the DbxRef This database name will be used if the DBxRef identification doesn t have a database scoreColumnIndex the number of the score column If there isn t a value in the column indicate by this parameter then the annotation object will not have a score methodColumnIndex the number of the method column If there is not a value in the column indicate by
12. d or source and annotation score Behind these well defined columns there is one column to put generic informations or attributes about the feature annotation using a list in the format tag name tag value We will call this list of feature attribute list This program can store in the database all types of entities except DBxRefDBxRefAnnotation and SubseqDBxRefAnnotation Behind the entities the program can create and store synonyms for Sequences Subsequences and SubseqFeatureAnnotations and notes for SubseqFeatureAnnotations The line command syntax is org cycads ui loader GFF3Loader lt fileName gt lt organismNumber gt lt organismName gt lt seqDBName gt lt seqVersion gt where fileName name and path of the GFF3 file to load organismNumber NCBI taxon ID of the organism to be loaded organismName name of the organism to be used when creating new organisms seqDBName database name of the sequence accession The sequence accession is in the first column of the GFF3 file One DBxRef object is created with the segDBName and accession to be a synonym of the sequence seqVersion the sequence version to be used when creating new sequences After these parameters the loader accepts many parameters by config properties to interpret the GFF3 file content and to transform it in the CycADS database format The parameter names in the config file follow this syntax GFF3Loader file attribute lt type gt lt source gt lt para
13. e folder when multiple PF files options is used see fileFormat parameter bellow organismNumber NCBI taxon ID of the organism which data will be extracted seqDbname seqAccession the sequence identification database name and accession of the sequence separated char will select all the sequences seqVersion a valid sequence version or all the versions of the sequence using the char sequenceLocation y or n as boolean char to export respectively sequence location or not ecThreshold annotation methods evidences for EC Enzyme Commission numbers are grouped in an EC annotation cluster when they are loaded So that EC cluster got a cumulative score for EC EC with a cluster score bellow the ecThreshold will not be extracted goThreshold the same as ECthreshold but for the GO 3 2 2 fileFormat 1 pf file 2 annotationByLine each line 1 GO EC KO etc annotation 3 functionByLine each line 1 CDS TRNA etc function 4 Multiple PF Files for example one per sequence returned by the char set for seqDbname seqAccession parameter Config properties CycADS can filter further using the config properties where many parameters can be set to produce a rich output for BioCyc databases Most of these parameters accept regular expressions and filters for the best flexibility Parameters names follow the same expression using defined types to simplify the properties writing The program call an object getter an
14. ef identifications column Given a line in the file for each pair Subsequence DBxRef identified one SubseqDbxrefAnnotation object is created The subsequence identification or subsequence DBxRef is a DBxRef which must be a subsequence synonym or an association synonym with the association source being a subsequence If the subsequence DBxRef don t reach a subsequence by the subsequence synonym or association synonym then the program will do nothing The line command is org cycads ui loader SubseqDbxrefAnnotationLoader lt fileName gt lt organismNumber gt lt methodName gt lt sourceColumnIndex gt lt sourceDBName gt lt targetColumnIndex gt lt targetDBName gt lt scoreColumnIndex gt lt methodColumnIndex gt where fileName name and path of the file to load methodName the default method name to be used to create the SubseqDbxrefAnnotation object This argument will be used only if there isn t one column to give the method name or the content of this column is blank or empty sourceColumnIndex the number of the subsequences identifications column sourceDBName the external database name of the subsequences identifications This database name will be used if the subsequences identifications doesn t have a database name targetColumnIndex the number of the DBxRef column targetDBName the external database name of the DbxRef This database name will be used if the DBxRef identification doesn t have a database name scoreColumnIndex
15. er file lt type gt tagOperation lt i gt lt op gt tagName regex and GBKLoader file lt type gt tagOperation lt i gt lt op gt tagValue regex match with respectively tag name and tag value of the tag The possible operations are e remove remove the tag of the feature tag list e split split the tag value string around matches of the regular expression given by the additional argument GBKLoader file lt type gt tagOperation lt i gt split separator regex e changeTagName replace the tag name by the string given by GBKLoader file lt type gt tagOperation lt i gt changeTagName newTagName argument e changeTagValue replace each substring of the tag value string that matches the regular expression given by the additional argument GBKLoader file lt type gt tagOperation lt i gt changeTagValue substSourceTagValue regex with the replacement given by the additional argument GBKLoader file lt type gt tagOperation lt i gt changeTagValue substTargetTagValue These additional arguments can be a list of arguments In this case the operation is executed for each pair GBKLoader file lt type gt tagOperation lt i gt changeTagValue substSourceTagValue regex lt j gt and GBKLoader file lt type gt tagOperation lt i gt changeTagValue substTargetTagValue lt j gt e copy create a new tag with the new tag name given by GBKLoader file lt type gt tagOperation lt i gt copy newTagName argument and the new tag value equal to the tag value
16. g the output message associated with the KOs functionGOs goMsg the output message associated with the GOs functionECs ecMsg the output message associated with the ECs dblinks and geneDblinks identification of data having to appear as dblink score apply to ko functionGOs and functionECs A default score method valueDefault and weighting method weight for each method defined in method regex can be set This is useful for filtering the output threshold a double value indicating the threshold for ec and go respectively Only ec or go annotations having a score higher than the value will be extracted scoreFilterByAnnotationType and methodFilterByAnnotationType respectively score and method can be filtered by type Function assignment or DbxRef assignment outFormat an integer which indicate the output format 1 pf file 2 annotationByLine each line 1 GO EC KO etc annotation 3 functionByLine each line 1 CDS TRNA etc function idNoteType the note id type CycID uses CycADS identification methodSeparator the separator string for the methods methodPathSeparator the separator string for the methods paths annotationScoreDefault double value for the default annoation score pf header the header of the generated PF file pf functionName function name or accession for the FUNCTION attribute in PF Files pf functionName loc where functionName are extracted from CycADS pf functionSynonyms loc where func
17. given by the annotation method In general the score represents the reliability of the annotation as assessed by an individual method o Parent optional indicates one or more parent annotations The parent annotations are the annotations one level higher than the current annotation Currently this attribute is used to describe the embedding of feature associations For example in the annotation of a given subsequence as being an mRNA the parent annotation is the annotation of the corresponding subsequence with the feature gene The annotation objects are classified according to the source and target types involved in the proposed assignment In the current version we use the following Annotation objects o SubseqAnnotation represents the annotations of the subsequences We have the following SubseqAnnotation objects e SubseqFeatureAnnotation represents one proposed assignment of a feature e g gene mRNA CDS etc to a subsequence SubseqDBxRefAnnotation represents one proposed assignment of an external reference e g EC GO etc to a subsequence e SubseqFunctionAnnotation represents one proposed assignment of a function e g xanthine dehydrogenase to a subsequence e DBxRefDBxRefAnnotation represents one proposed assignment of a DBxRef to another DBxRef e g to assign an EC number to a KO Kegg Ontology number o AnnotationMethod the method used to generate an annotation All basic entities can have multiple externa
18. gment defined by a set of positions on a sequence indicating the beginning and the end of the fragment on the sequence as well as the beginning and end of the intron s where it applies DBxRef reference to an object in an external database It has the attributes DBName and Accession and in general it is written as DBName Accession The DBName is the name of an external database while Accession is the identification of the current object in the external database For example in the DBxRef EC 1 1 1 1 the DBName EC Enzyme Commission and the Accession 1 1 1 1 Function the name or description of a biological function such as alcohol dehydrogenase Feature the nature of a subsequence such as mRNA gene CDS etc Association represents a relationship between 2 objects s source and target of basic entities We say that s is associated to t We can classify the associations and store the type s of each association Currently we are using this entity to represent the parent relationship of annotation objects described below Annotation a specific case of association where the relationship between the two associated objects is uncertain It is used when an annotation method tentatively assigns a basic database entity object to another basic database entity object An Annotation has the following attributes o Method the annotation method that suggested the association o Score optional the score of the association as
19. is the source SO Source TA Target AY Annotation Types ME Method SC Score EN End BE Begin NA Name OR Organism SE Sequence VE Version SS Subsequence TY Entity Type SY Synonym NO Note NT Note Type NV Note Value DB Database Name DbxRef AC Accession DbxRef ST to String All SI Size of Sequence the char ask to the program to get a data object using the expression filter expressions lt comparison operator gt lt string value gt comparison operator lt gt lt lt gt gt gt lt string value a defined type or another regular expression 3 3 Auxiliary programs org cycads ui tools CleanColumn lt fileName gt lt cleanColumnIndex gt lt columnSeparator gt lt lineComment gt lt cleanExpression gt lt outputFileName gt This tool can clean the indicated column using the cleanExpression regular expression org cycads ui tools RemoveLineStringColumn lt fileName gt lt removeColumnIndex gt lt columnSeparator gt lt lineComment gt lt removeExpression gt lt outputFileName gt This tool can remove the lines using the removeExpression regular expression matching in the indicated column org cycads ui tools RetrieveStringColumn lt fileName gt lt retrieveColumnIndex gt lt columnSeparator gt lt lineComment gt lt retrieveExpression gt lt outputFileName gt This tool can retrieve the lines using the retrieveExpression regular expression matching in
20. l names stored as synonyms using DBxRef objects and can have multiple simple notes stored as text The notes have a note type and a text value 3 The programs The CycADS programs can be executed at the command lines A program uses parameter values or arguments passed on the command lines and in the file config properties to get all the information necessary to its execution The following subsections will describe these commands and their parameters We have established a pattern for the name of the parameters in the config properties file In general a line in the config properties follows this syntax lt program name gt file lt parameter specificity gt regex lt i gt lt value gt where e lt program name gt is the name of the program or the word general if the parameter will be used by many programs e file indicates that the parameter value is related to a file specification e lt parameter specificity gt is a name that will specify the parameter In general it will indicate its usage e regex indicates that the program expects a regular expression e lt i gt is a number between 0 and 2 6 1 used when the program expects to receive a list of arguments for the parameter lt program name gt file lt parameter name gt regex The number 7 indicates the position of lt value gt in this list of arguments If the list does not have the value at the position i then the value at the position i will be not treated by
21. lt i gt if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt parentAccessionTag regex then the tag value of this attribute will be used as accession of a DBxRef to try to find an annotation object to be the parent of the SubseqFeatureAnnotation object The DBName of the DBxRef will be the argument GFF3Loader file attribute lt type gt lt source gt parentDbName lt i gt and the DBxRef must be a synonym of the parent annotation object GFF3Loader file attribute lt type gt lt source gt noteTypeTag regex and GFF3Loader file attribute lt type gt lt source gt noteTypeValue lt i gt if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt noteTypeTag regex lt i gt then a note will be add to the SubseqFeatureAnnotation object The note type will be GFF3Loader file attribute lt type gt lt source gt noteTypeValue lt i gt and the note value will be the tag value GFF3Loader file attribute lt type gt lt source gt functionTag regex and GFF3Loader file attribute lt type gt lt source gt functionMethodName if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt functionTag regex lt i gt then a SubseqFunctionAnnotation will be created with the function name equals to the tag value and the annotation method name equals to GFF3L
22. meter specificity gt regex lt i gt Moreover the name parts described in the beginning of this section we have lt type gt or feature config type name means that the respective argument is applied only to features of the type lt type gt lt source gt means that the respective argument is applied only to features where source the second column in the GFF3 file is equal to lt source gt attribute is used if the argument is relative to the list of feature attributes in the GFF3 file The parameters in the config properties are GFF3Loader loader fileName the same as the fileName line command parameter GFF3Loader loader organismNumber the same as the organismNumber line command parameter GFF3Loader loader organismName the same as the organismName line command parameter GFF3Loader loader sequenceDbName the same as the seqDBName line command parameter GFF3Loader loader sequenceVersion the same as the seqVersion line command parameter GFF3Loader file geneConfigType GFF3Loader file exonConfigType GFF3Loader file rnaConfigType and GFF3Loader file cdsConfigType for each feature annotation type gene RNA CDS and exon indicate the type name to use in the parameter names in the config properties This type name will be stored also in the database as a feature object GFF3Loader file lt type gt type regex if GFF3Loader file lt type gt type regex matches with the type name of the feature annotation to be load then the
23. n include large amino acids or nucleotides sequences data you will probably have to set your SGBD specifications depending on the client or server SGBD used and the size of the data you want to collect For MySQL it is necessary to increase the value of the max_allowed_packet variable http dev mysql com doc refman 5 0 en packet too large html at least 16M or more Download and install the corresponding JDBC driver Connector J 5 1 X for the MySQL choice http www mysql com downloads connector j 5 1 html Create an empty database and a user with grant privileges on it Then execute the SQL script cycads1 3 sql provided in the software package to build the CycADS database schema SQL instructions are added for automatic triggers at the end of the script They are optional with the current release 1 3 of CycADS Download CycADS package at http pbil univ lyon1 fr software cycads cycads zip Download CycADS external libraries at http pbil univ lyon1 fr software cycads libraries zip Unzip the CycADS software package in a directory of your choice and the libraries archive in the same directory The connection parameters to the CycADS DB have to be set in the config properties file general sql driverName your DBCdrivername com mysql jdbe Driver for MySQL general sql connectionUrl jdbc vourSGBD server port yourdatabasename ie _ jdbc mysql Nocalhost 3306 cycads general sql usr yourusername general sql pass youruserpass Set up the co
24. name to be used to create the DbxrefDbxrefAnnotation object sourceColumnIndex the number of the entity identifications column sourceDBName the external database name of the entity identifications This database name will be used if the subsequence identification doesn t have a database name targetColumnIndex the number of the DBxRef column targetDBName the external database name of the DbxRef This database name will be used if the DBxRef identification doesn t have a database scoreColumnIndex the number of the score column If there is not a value in the column indicate by this parameter then the annotation object will not have a score methodColumnIndex the number of the method column If there is not a value in the column indicate by this parameter then the method name of the annotation object will be the method name default indicated in the methodName parameter The parameters in the config properties are The same as above which will be used when they are missing in the command line parameters Note that confirmation is asked to the user with an input dialogbox Additional parameters about the file format can must be set such as column separator line comments chars and so on EntitySynonymLoader This program loads EntitySynonym objects created from a text file with columns delimited by a string The column delimiter string is given by one parameter in the config properties file The file must have at least 2 columns the Entity ide
25. nd Accession of the DBxRef are in the tag value separated by GFF3Loader file attribute lt type gt lt source gt annotationCompletSynonymSeparator GFF3Loader file attribute lt type gt lt source gt annotationSynonymAccessionTag regex and GFF3Loader file attribute lt type gt lt source gt annotationSynonymDbName if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt annotationSynonymAccessionTag then the tag value of this attribute will be used as accession of a DBxRef to assign a synonym to the SubseqFeatureAnnotation object The DBName of the DBxRef will be the argument GFF3 Loader file attribute lt type gt lt source gt annotationSynonymDbName GFF3Loader file attribute lt type gt lt source gt subsequenceSynonymAccessionTag regex and GFF3Loader file attribute lt type gt lt source gt subsequenceSynonymDbName if the tag name of a attribute of the feature matches with GFF3Loader file attribute lt type gt lt source gt subsequenceSynonymAccessionTag then the tag value of this attribute will be used as accession of a DBxRef to assign a synonym to the Subsequence object The DBName of the DBxRef will be the argument GFF3Loader file attribute lt type gt lt source gt subsequenceSynonymDbName GFF3Loader file attribute lt type gt lt source gt parentAccessionTag regex and GFF3Loader file attribute lt type gt lt source gt parentDbName
26. nfig properties file in accordance with the data you want to load and or extract Launch the CycADS AnnotationCollector program or later the AnnotationExtractor you need respectively loaders and extractors described previously using the command line java Options cycads1 3 jar biojava jar bytecode jar mysql connectorjava 5 1 6 bin lt programName gt lt programParameters gt with Options Java options commonly Xmx512M cp Memory consumption has generally to be set between 512M and 2048M depending on the data size See also http java sun com javase 6 docs technotes tools windows java html programName one Loader or Extractor as described in section 3 of this manual programParameters the parameters as in the corresponding program description or by modifying the script cycads1 3 sh to launch most of the loaders and extractors with provided data examples http pbil univ lyon1 ft software cycads example_tricacyc zip 7 Troubleshooting Java will generate error numbers and descriptions to the standard output The error messages can help to solve the problems 8 Future works Graphic user interface control of the config properties parameters Delete records or undo loads Config operations standard for gff3 and gbk loaders PFFileGenerator don t follow differents structural annotations Plugin or connector for metabolic networks software such as MetExplore
27. ngeType newValue lt i gt if GBKLoader file changeType regex i argument matches with the type name of a feature in the genbank file then the type name of this feature will change to GBKLoader file changeType newValue i GBKLoader file changeConfigType regex lt i gt and GBKLoader file changeConfigType new Value lt i gt these parameters are used to get the feature config type name the word lt type gt in the parameter name If GBKLoader file changeConfigType regex i argument matches with the type name of a feature in the genbank file then the feature config type name of this feature will change to GBKLoader file changeConfigType newValue i For instance if we set GBKLoader file changeConfigType regex i RNA and GBKLoader file changeConfigType newValue i RNA then we can group all feature types that finish with the word RNA like mRNA ncRNA tRNA etc and treat them with the same parameters in the config properties file GBKLoader file lt type gt methodName indicates the name of the annotation method used when creating an entity SubseqFeatureAnnotation GBKLoader file lt type gt tagOperation lt i gt this parameter says the operation to execute in the tag name or tag value of a tag in the genbank file The operation lt i gt is executed after the operation lt i 1 gt The arguments or operations can be remove split changeTagName changeTagValue and copy An operation op is executed over a tag if the additional arguments GBKLoad
28. notation cluster for each parameter This object getter can extract annotation data through the location loc indicated make changes or get another filtered object Parameters names definition AnnotationGenerator lt fileformat gt lt parameter name gt lt type gt lt method gt loc regex lt i gt where lt fileformat gt indicates that the parameter value is related to a file specification pf apply to PFFile specification lt type gt or feature config type name means that the respective argument is applied only to features of the type lt type gt lt parameter name gt means that the respective argument is applied only to object fileName the same as the command line first organismNumber the taxon id of the organism sequenceSynonym a sequence synonym in the database or for all sequences sequenceVersion the sequence version to be extracted feature the name of the considered features ie CDS RNA productType product type and changes operations on it which can be made in accordance with the target output format location replace regex replace replacement geneName the accessions of the genes location of gene data geneSynonyms the accessions of the gene synonyms location of gene synonyms data geneAnnot the location of the gene annotations location of gene annotations geneComments the comments or output messages associated with the genes ko the accessions of the KOs koMs
29. ntifications column or Entity DBxRefs column and the Synonym identifications column Given a line in the file for each pair Entity Synonym identified one EntitySynonym object is created The Entity identification is a DBxRef which must be an entity synonym If the Entity DBxRef don t reach an entity synonym then the program will do nothing The line command is org cycads ui loader EntitySynonymLoader lt fileName gt lt sourceColumnIndex gt lt sourceDBName gt lt synonymColumnIndex gt lt synonymDBName gt where fileName name and path of the file to load sourceColumnIndex the number of the entity identifications column sourceDBName the external database name of the entity identifications This database name will be used if the entity identification doesn t have a database name synonymColumnIndex the number of the Synonym column synonymDBName the external database name of the Synonym This database name will be used if the Synonym identification doesn t have a database These parameters can be set in the config properties DbxrefSynonymLoader This program loads DbxrefSynonym objects created from a text file with columns delimited by a string The column delimiter string is given by one parameter in the config properties file The file must have at least 2 columns the Dbxref identifications column and the Synonym identifications column Given a line in the file for each pair Dbxref Synonym identified one DbxrefSynonym object is
30. oader file attribute lt type gt lt source gt functionMethodName lt i gt KOLoader This program loads data from a specific file from KEGG ftp ftp genome jp pub kegg genes ko This program will create a DBxRef to represent each KO record in the file This KO DBxRef object has the dbname equals to KO and the accession equals to the first six characters in the entry field of the KO record If there is an EC number in the definition field of the KO record then the program will create a DBxRefDBxRefAnnotation object to represent this link KO to EC Other DBxRefDBxRefAnnotation object will be created for each external reference objects in the DBLinks field of the KO record The text in the definition field except the EC numbers references will be stored as the definition note of the KO DBxRef object The line command is org cycads ui loader KOLoader lt fileName gt where fileName is the name and path of the KO file to load The parameters in the config properties are KOLoader fileName the same as the fileName line command parameter KOLoader ECAnnotationMethodName the annotation method name of the DBxRefDBxRefAnnotation object created to represent the link KO to EC numbers KOLoader DBLinkMethodName the annotation method name of the DBxRefDBxRefAnnotation object created to represent the link with others external reference objects except EC KOLoader file DBLink dbName regex lt i gt and KOLoader file DBLink newDbName lt i g
31. qDbxrefAnnotationLoader assocTypeName the association type Function assignment subseqDbxrefAnnotationLoader file sourcesDelimiter the delimiter string for the sources identifications subseqDbxrefAnnotationLoader file targetsDelimiter the delimiter string for the targets identifications subseqDbxrefAnnotationLoader file sourceColumnDelimiter the delimiter string for the sourceColumn subseqDbxrefAnnotationLoader file targetColumn Delimiter the delimiter string for the sourceColumn subseqDbxrefAnnotationLoader file scoreDelimiter the delimiter string for the score subseqDbxrefAnnotationLoader file methodDelimiter the delimiter string for the method name subseqDbxrefAnnotationLoader file lineComment the string which indicate a comment line subseqDbxrefAnnotationLoader file columnSeparator the string of the column separator subseqDbxrefAnnotationLoader file sourcesSeparator the separator string of the sources identifications subseqDbxrefAnnotationLoader file targetsSeparator the separator string of the targets identifications subseqDbxrefAnnotationLoader file removeLineRegex the regular expression defining the pattern for the matching lines to remove EntityDbxrefAnnotationLoader This program loads EntityDbxrefAnnotation objects created from a text file with columns delimited by a string The column delimiter string is given by one parameter in the config properties file The file must have at least 2 columns the entity identifications
32. stem We can split this layer in 2 packages Database storage The classes responsible to store and retrieve the data from to the repository Currently we are storing the data in a SQL database system and we are using SQL queries and SQL commands in the classes of this layer Database access Represents logically the data and is the interface to access this layer With the existence of this package we can change the way the data is stored database storage package without interfering with the other layers We are using Java interfaces to develop this layer Logical This layer coordinates the commands requested makes logical decisions and interacts with the data layer This layer includes the information and logic to parse several different data format User interface This layer makes the interaction with the users It gets the data provided by the users triggers the logical processes and presents the data generated by the system Currently the user passes information to CycADS or arguments of the system through the command line parameters and through the config properties file 2 The CycADS database We have some basic entities stored in the CycADS database which are Organism an organism Sequence a chromosome or contig of the organism for a given genome assembly with information about the assembly version The objects of this entity can also include the DNA sequence but this is not mandatory Subsequence reference to a sequence fra
33. t these parameters are used to change the DBName of a DBxRef created to represent a external reference object in the DBLink field of the KO record in the KO file If KOLoader file DBLink dbName regex lt i gt matches with a DBName in the DBLink field of the KO record in the file then the DBName to be stored will be KOLoader file DBLink newDbName lt i gt There are others parameters in the config properties to configure the file format and must be changed only if the KO file format is changed In the case of the KO file format is changed please try to get the newest version of CycADS or contact the support The following loaders programs are programs to create annotations to DBxRefs or to create synonyms The program load text files with columns delimited by a string e g tab caracter It is mandatory to specify two columns source column and DBxRef column The source column must have the DBxRefs to identify the source entities The source entity type change accordingly the loader program For the programs that create annotation objects we can have more two columns score column and method column SubseqDbxrefAnnotationLoader This program loads SubseqDbxrefAnnotation objects created from a text file with columns delimited by a string The column delimiter string is given by one parameter in the config properties file The file must have at least 2 columns the subsequence identifications column or subsequence DBxRefs column and the DBxR
34. the indicated column org cycads ui tools SplitFastaFile lt fileName gt lt searchColumnIndex gt lt columnSeparator gt lt searchExpression gt lt outfileExtension gt This tool can split a multifasta file using a regular expression matching in the indicated column of fasta headers strings It uses the regular expression matches for the outfiles names 4 Usage examples As show in T castaneum config properties example file provided in the package AnnotationGenerator pf geneName loc 0 PA PA SY db TCOGS2 AC This gets the accession of the gene synonyms grandparents synonyms of the features in the TCOGS2 database AnnotationGenerator pf geneName loc 1 PA TA ST i Gene S Y db T COGS2 AC This gets the accession of the gene synonyms parents synonyms of the features in the TCOGS2 database where feature have a Gene like parent feature 5 System requirements Java Runtime 1 6 SQL database Management system access External libraries biojava bytecode 6 Installation Download and install Java Runtime 1 6 if not existing in your system http java sun com javase downloads index jsp Download and install one SGBD for example MySQL http www mysql com downloads mysql Note that the use of MySQL is not mandatory other SGBDs can be prefered you have to define the JDBC driver and the connection string in the config properties although we didn t have done any tests on other systems Because annotation files ca
35. tion synonyms are extracted from CycADS pf functionComments loc where function comments are extracted from CycADS pf functionSSequence loc where function subsequences are extracted from CycADS pf AnnotationGenerator pf sequenceLocation exports the sequence location to PF Files or not y n pf AnnotationGenerator pf geneComment separator the separator of genes comments for the PF File output pf AnnotationGenerator pf functionComment separator the separator of functions comments for the PF File output lt loc gt the field location where the object getter can find the data lt type gt the scope of the parameter regarding the feature CDS TRNA MISCRNA lt method gt the scope of the parameter regarding the method regex used when the program expect a regular expression lt i gt an integer value between 0 and 2 6 when the program expect a list of arguments Parameters values They can be double integer or string Regular expressions are built using locType P Parent FA FunctionAnnotation XA dbxrefAnnotation SY Synonym NO Note SE Sequence SS Subsequence F Function V NoteValue or Dbxref accession or Function Name XV Dbxref of dbxrefannotation XR lt name gt set of dbxrefs Other expression types are defined to use in the syntax of the parameters values and get objects in accordance with the program state machine AT Annotations where Entity is the target AS Annotations where Entity

CycADS User Manual

Contents

Download Pdf Manuals

Related Search

Related Contents