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BioXM™ Knowledge Management Environment

1. Figure 61 Creating a query displaying refined query results 39 Quick Start 6 The results include all genes which are assigned the GO 0007165 signal transduction entry and all genes which are assigned entries derived from the signal transduction entry 1881 objects in total 3 6 Saving the query and creating a smart folder 1 Click the Next gt button in the Search results window to save the query and create a smart folder The Save query window will be displayed amp Find by advanced query BioXM ls pa Ww Define Query Save query V Save query w Search Results Name Find signal transduction genes v Save query 7 Create smart folder in 8 ma Create new folder xs New folder will be created in top level of project Public Folder class GeneralFolder v Folder name My queries cance Save query template Save query template Figure 62 Saving the a query and creating a smart folder 2 Click the Save query check box and enter a name e g Find signal transduction genes for the query 3 Click the Create smart folder in check box Select the Public folder and click the Add Folder button 4 Enter a name for the folder My queries and click OK to close the dialog 5 Click the Finish button to close the query wizard The My queries folder containing the Find signal transduction genes smart
2. Q Assign object shape E Do not trim surrounding spaces Rename annotation vete Annotation and Meta data Split with separator Create annotation T Tab Q Assign annotation Lookup annotation Custom Change annotation Q Detach annotation Reg ex E L0 M Teeetoe eme ESSR a Show description Add gt gt Add Delete b y Overview Variables Name Type Value Add Data preview Click a column to select it A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid 2 palla E53 3 76P Homo sapiens 4 A16 Homo sapiens A21 Homo sapiens AWA ama naminal 129938 15E 1 2 MGC 129938 15e1 2 283459 GO 0017068 GO 0000004 GO 0005554 G CP4 FLJ14797 GCP4 76P TUBGCP4 gam 27229 G0 0000226 GO 00058 15 GO 0000922 G A 1B ABG GAB HYST2477 DKFZp686F0970 1 GO 00 16020 GO 0000004 GO 0005554 G T OX 1 HRNBP 1 FOX 1 HRNBP 1 A2BP 1 a2b 54715 d 770bn29z le c ereclabulinasleb 12 GO 0000 166 GO 0003723 GO 0005515 G lceuannaec ceo anakg3e co nnnzesz c lt Back Next Finish cancel 19 Figure 33 Importing data tab import script Lookup or create element operation Quick Start 2 Under Available import operations select Create annotation and click the Add gt gt button Options for the import operation will be displayed under Tab import script
3. Show description Variables Name Figure 51 Creating a view reordering the view items 34 Quick Start 11 Click the OK button to close the dialog In the Global Views dialog click the Close button G BioXM Knowledge Management Environment X3 Global Views Project Object Type Public Element Gene Description Table C Enabled Table Default Yes Report Default Yes Report i Gene list view C Enabled Figure 52 Global Views dialog 3 2 Displaying the view To display the new view select Gene list view from the View drop down menu in the Gene element window p gt BioXM Knowledge Management Environment File Edit View Settings Modeling Administration Search Tools Help Gene Element Type View 1 Q Public Repositories amp M Annotations E Basic information BioRS entries E EntrezGene H E UNIPROT_SPROT S i Elements Ej E Protein S i Ontologies E Element general information iBi Gene list view 15E1 2 Homo sapiens 76P Homo sapiens A 1BG Homo sapiens A2BP 1 Homo sapiens A2M Homo sapiens A2ML 1 Homo sapiens A3GALT2 Homo sapiens A4GALT Homo sapiens A4GNT Homo sapiens AAAS Homo sapiens A13 Homo sapiens 16 459 object s aa Y Graph Folder
4. Annotate Current project Public Figure 53 Element general information view selecting a new view In the view the columns can be sorted by clicking any column header e g Chromosome Columns can be selected to be displayed or not by clicking the table icon in the top right corner of the table gt BioXM Knowledge Management Environment File Edit View Settings Modeling Administration Search Tools Help 2 Gene Element Type View General Elements f Annotations E Basic information Ven ED Genet nase BioRS entries or E EntrezGene f H E UNIPROT SPROT Gens x r gcach Elements FA E Gene Synonyms EntrezGene Chromosome GO 3 5 Protein 15E1 2 Homo sapiens MGC129938 283458 12 L3 G0 0006450 requlation of translational fidelity E H Ontologies ee EN H E co hypothetical protein loc283459 Queries mgc129938 f Relations c 129938 E encoding ypothetical protein loc 283459 Functional Classification ypothetical protein loc 283459 c 129938 B 76P Homo sapiens ca 27229 15 LI G0 0000226 microtubule cytoskeleton organizat 14797 L3 G0 0005815 microtubule organizing center QR LI GO 0000922 spindle pole amma tubulin ring complex protein 76p gene LI G0 0005200 structural constituent of cytoskeleta fe Aper 0 60 0005813 centrosome ithe 76p protein LI GO 0005874 mi
5. 2 O 0004867 GO 0005576 GO 0 CPAMDS FLJ16045 FLJ25179 FL 144568 0 0004866 A3GALT2 a 1 3 galactosyltransf 127550 O 0005975 GO 0016020 GO 0 P1 PK A14GALT A4GALT 1 PK A4 53947 O 0005624 GO 0005795 GO 0 Figure 31 Importing data defining the physical layout 4 Select the New script option and click the Next button to continue to the Define Tab Import Script step of the import wizard amp BioXM Knowledge Management Environment Import Table Data Current Step Choose Script Kind Create the new script from scratch Existing script Choose a script stored in the database Data preview A Gene Name B Synonyms D GO Ontology entry Uid 2 15E1 2 Homo sapiens 129938 15E 1 2 MGC 129938 0 0017068 GO 0000004 GO 0 3 76P Homo sapiens CP4 FLJ14797 GCP4 76P TUBG 27229 O 0000226 GO 0005815 GO 0 4 A1BG Homo sapiens A 1B ABG GAB HYST2477 DKFZp 1 O 0016020 GO 0000004 GO 0 5 A2BP1 Homo sapiens OX 1 HRNBP 1 FOX 1 HRNEP 1 A2 O 0000166 GO 0003723 GO 0 6 A2M Homo sapiens dkfzp779b086 alpha 2 macroglo 2 O 0004867 GO 0005576 GO 0 7 8 9 10 1 Homo sapiens CPAMDS FLJ16045 FLJ25179 FL 144568 0 0004866 A3GALT2 Homo sapiens A3GALT2 a 1 3 galactosyltransf O 0005975 GO 0016020 GO 0 A4GNT Homo sapiens 0c51146 a4gnt mgc149493 alph 11 JAAAS Homo sapiens AAA AAASb GLOO3 ADRACALA 808
6. 27229 O 0000226 GO 0005815 GO 0000922 G c A 1B ABG GAB HYST 2477 DKFZp686F0970 O 0016020 GO 0000004 GO 0005554 G FOX 1 HRNBP 1 FOX 1 HRNEP 1 A2BP 1 a2bp O 0000 166 GO 0003723 GO 0005515 G X ETS Bak Next Fish Figure 37 Importing data tab import script Lookup or create relation operation Before continuing we will store the import script Click the Store as button at the top of the import wizard Enter a name for the tab import script in the dialog and click the OK button to return to the wizard Create new tab import script New tab import script will be created Name Import gene index table Figure 38 Importing data storing the import script Click the Next button in the import wizard to continue to the Choose Processing Policy step 23 Quick Start 2 3 Simulating the import First we will simulate the import using the first 100 items to make sure the import script works as needed Then we will import the entire table P gt BioXM Knowledge Management Environment Import Table Data Current Step Choose Processing Policy Allow partial import Commit changes for errorless import operations by small portions 5 Allow complete import only Do not commit any changes if any errors were found Simulate import Do not commit any changes even on successfull import Stop after the specified number of errors
7. 7 biomax E r Welcome to the Biomax Knowledge Portal 3 O 8e Home First time users get a tour introducing the BioXM portal builder here For personal settings change your preferences Administrators if the data model has changed hit BioxmRefresh Sit TUE Queries of interest e FindSignalTransductionGenes Figure 72 Displaying a new topic in the WebHome page Click the question mark next to the FindSignalTransductionGenes text to edit the new page The Foswiki editing interface for the new page which is similar to the WebHome editing interface will be displayed We will edit the page to include a heading called Find signal transduction genes and a BioXM plugin to list the content of the smart folder of that name Listing the contents of smart folders i e executing BioXM queries is done using the following general plugin call SBIOXM_QUERY query query_name 45 Quick Start More information about the plugin syntax used in the BioXM Web Portal Builder can be found on the BioXM Support Web https ssl biomax de info biomax bin view BioXM PortalBuilderReference To add the Find signal transduction genes query enter the following text Find signal transduction genes S6BIOXM_QUERY query Find signal transduction genes Find Signal TransductionGenes new v Text Settings Help Title FindSignalTransductionGenes H H2H3H4 A AAA FA E Find signal transduction genes
8. Annotation Co basic EN nde Gene Protein encoding database database mapping mapping UniProt Figure 1 Sketch of a data model 1 1 Starting the BioXM system To start the BioXM client complete the following steps 1 Start the BioXM client e g by entering the uniform resource locator URL of your BioXM instance in a browser The login page will be displayed 2 Enter your user name and password and click the Login button The BioXM Knowledge Management Environment application will start and the main application window will be displayed Quick Start gt BioXM Knowledge Management Environment istration Search Tools Help File Edit View Setting i Hello biomax Current Project Public Version 4 0 232 06 06 4 B Helping you get the most p out of your data and resoure y i 1 gt y A HL i BioXM Knowledge Management Environment e biomax gt biomak infonmotics og www biomax com biomax informatics ai Current project Public Figure 2 BioXM main application window 1 2 Displaying the data model The BioXM system provides a graph viewer for visualization of semantic objects and the connections between them as well as exploration of the resulting semantic network or data model The BioXM graph viewer renders the data model as an interactive white board so semantic objects and associated o
9. Our data model is in principle complete Before we import data into it we will save the layout for future access 1 Click the Save graph state button in the top right corner of the window to display the Save Graph State dialog ij Save Graph State a Save as new My Model Figure 27 Naming the data model layout 2 Enter a name for the model e g My Model in the Save as new field and click the OK button The data model layout is saved and can be subsequently selected for display in the data model graph 1 11 Displaying a saved data model layout The saved data model layout can be selected for display as follows 1 Select Modeling Visualize Data Model in the main menu to display the Visualize Data Model window 15 Quick Start j BioXM Knowledge Management Environment Visualize Data Model Annotation Annotation Basic information BioRS entry BioRS entry EntrezGene BioRS entry UNIPROT_SPROT BioRS entry UNIPROT_SPROT features BioRS entry UNIPROT_SPROT references BioRS entry UNIPROT_SPROT remarks Element Element Gene Element Protein Ontology entry Ontology entry GO Relation Figure 28 Selecting a saved layout for display Click the Saved visualization option and select the My Model layout from the drop down menu Click OK to display the data model graph with the selected layout 6 Data Model Graph BioXM E Align 100 Layout Grap
10. i Assign BioRS entr BJ Name pe BioRS ail f Form 8 Basic information doniniogy eni Xj Get assigned annotations MJ Overwrite Yes E 6 ddp ruis Q Create in project C Dedine empty object set BY oop or eate relation 5 6 Attributes Q Transfer relations BJ Synonyms B Synonyms Qi Lookup or create context B 3 Lookup and assign BioR Add object to context BJ Object element1 Q Add relation to context BJ Databank EntrezGene i Remove object from context Hj Element name ge is 3 Data Deletion B Element value C EntrezGene ID Z Delete object M Skip lookup by ID Yes Q Delete object alias 4 Lookup ontology entry Sontology entry1 Q Delete object shape E BI Ontology Go Project and Resource Maintenance BJ Lookup by uid Move object to project i R3 Value D GO Ontology entry Uid Add object to folder j Q 5 Lookup or create relatic relation Q Create folder ft Relation dass Functional Classification 5 Q Execution Control Q Finish script H7 Target element1 P Execution control if Create in project Add gt gt Add Delete a Vv Overview Variables ane Type Value Add Data preview A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid 2 15E1 2 Homo sapiens MGC129938 15E 1 2 MGC 129938 15e 1 2 h 283459 GO 0017068 GO 0000004 G0 0005554 G a 3 76P Homo sapiens GCP4 FL314797 GCP4 76P TUBGCP4 gam
11. 1000 S Process only lines 100 Comma separated list of ranges each in the form from to either end may be omitted Example 10 20 30 40 50 7 V Produce import log Record all import operation activity for each table row A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid 2 15E1 2 Homo sapiens 129938 15E 1 2 MGC 129938 15e 1 2 h 283459 GO 0006450 3 76P Homo sapiens 4 FLJ14797 GCP4 76P TUBGCP4 gam 27229 15 G0 0000922 G co 1B ABG GAB HYST 2477 DKFZp686F 0970 1 0016020 GO 0005576 5 A2BP1 Homo sapiens X 1 HRNBP 1 FOX 1 HRNBP 1 A2BP 1 a2bp 54715 GO 0000 166 GO 0003723 GO 0005515 G fzp779b086 alpha 2 macroglobulin alph 2 GO 0004867 GO 0005576 GO 0006886 G AMD9 FLJ16045 FLJ25179 FL J39129 FL 144568 3GALT2 a 1 3 galactosyltransferase 2 is 127550 0005975 GO 0016020 GO 0016758 3 Du A ACAL TUA AC Lir 3043 8 A3GALT2 Homo sapiens Figure 39 Importing data choosing a processing policy to simulate the import 1 Click the Simulate import radio button 2 Click the Process only lines check box and set a number of lines to process e g 100 to simulate the first 100 lines or leave the check box empty to simulate the entire import 3 Click the Produce import log check box to record all import operation activity for each line
12. Duplicate fede6 L3 G0 0005634 nucleus Gurt nac G0 0006260 DNA replicati sede 18 LJ GO 0007049 cell cycle kdc 6 LI G0 0007067 mitosis kdc vi L G0 0008285 negative requ kdc vi LJ G0 0017111 nucleoside tr 18l LJ G0 0051301 cell division scdc 6 scdc vi 18l scdc 18 6 scdc 6 scdc vi sCDC6 CDT Homo sapiens edt 81620 16 G0 0005634 nucleus rr parked drosophila homolog of O G0 0000076 DNA replicatid kdt E indi L 60 0003677 DNA binding c acie O G0 0005515 protein bindi unc ics ard dba replication L1 60 0005657 TIT 1 O 60 0006260 DNA replicati is2 O G0 0007049 cell cycle dup protein LJ 60 0030174 regulation of l ti ti dup gene ti omatin licensing and dna replication 1 881 object s M s xv Export Graph List Folder Annotate Smart folder Find genes by function Current project Public Figure 65 Selecting a smart folder to edit in the project tree 41 Quick Start 3 We will edit the query to create a more general query to find genes by functions specified by a GO term In the Object to find panel select the criteria like signal transduction to display the like panel on the right In the right panel check the Use variables check box and click the Introduce variable button gt BioXM Knowledge Management Environment Object to find Analyze query is a Gene which is dassified by a GO entry whid is inferred by ontology ent has
13. Rename anmotation J eyed ma assign BioRS a Do not trim surrounding spaces Annotation and Meta data P je Selemen V SP QG Create annotation i 8 Databank EntrezGene V Split with separator Assign annotation HD Element name L todas BJ Element value C EntrezGene ID Q9 Preset E Change annotation i Skip lookup by _ID_ Yes mum Detach annotation 4 Lookup ontology entry Sontology entry1 Transfer annotations 8j PAN L eo 7 Lookup and assign BioRS entry Lookup by Uid Post processing options Edit gt Get assigned BioRS entries D GO Ontology entry Uid No special options selected tQ Assign BioRS entry Show description Add gt gt y Overview Variables Name Type Value Add Data preview Click a column to select it A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid goto Pee sapien _3 76P Homo sapiens MGC 129938 15E1 2 MGC129938 15e 1 2 h GCP 4 FL314797 GCP 4 76P TUBGCP4 gam g GO 0017068 G0 0000004 G0 0005554 6 GO 0000226 GO 00058 15 G0 0000922 G 4 A18G Homo sapiens A 1B ABG GAB HYST2477 DKFZp686F0970 GO 0016020 GO 0000004 GO 0005554 G 5 A2BP 1 Homo sapiens tie FOX 1 HRNBP 1 FOX 1 HRNEP 1 A2BP 1 a2bp GO 0000 166 GO 0003723 GO 0005515 G Bak Next cand Figure 36 Importing data tab import script Lookup ontology entry ope
14. TIL i i PI hi hill Hl BIOXM QUERY query Find signal transduction genes Main BiomaxAdmin 12 Mar 2011 w Save Save and Continue Preview 3 Cancel Force new revision Figure 73 Adding the query plugin Click the Save button The edited FindSignalTransductionGenes page will be displayed amp Biomax Admin Users LogOut The BioXM Knowledge Portal You are here BioXM Find SignalTransductionGenes 1881 items found E G oz dG amp P The bio max BM tics og Find signal transduction genes Home Gene Rows 25 v Page 1 of 76 Prev Next 3 Sitemap CDC6 Homo cdc6 related protein 990 3 G0 0007089 traversing start control point of mitotic cell cycle sapiens cdc cell division cycle 6 homolog s cerevisiae 1 GO 0008156 negative regulation of DNA replication cdc6 cell division cycle 6 s cerevisiae homolog 3 G0 0000166 nucleotide binding hscdc18 D GO 0000076 DNA replication checkpoint hscdc6 O G0 0005737 cytoplasm cdc18 cell division cycle 18 s pombe homolog like D GO 0000079 regulation of cyclin dependent protein kinase activity cdc6 O G0 0005515 protein binding cdc6 homolog D GO 0005524 ATP binding cdc18l O G0 0005634 nucleus hscdc 18 3 G0 0006260 DNA replication cdc 6 C G0 0007049 cell cycle cdc vi O G0 0007067 mitosis cdc vi Oo GO 0008285 negative regulation of cell proliferation cdc 18l 1 GO 0017111 nucleoside triphosphatase activity hscdc 6 O G0 0051301 cell division hscdc v
15. binding a me G0 0000078 DNA replication checkpoint pedi L GO 0005737 cytoplasm scdc6 L GO 0000079 regulation of cyclin dependent protein ki cdc 18 cell division cyde 18 i GO 0005515 protein binding S pombe homolog like O 60 0005524 ATP binding kdc O 60 0005634 nucleus ires 60 0006260 DNA replication Es di G0 0007043 cell cycle kdc 6 L GO 0007067 mitosis cdc vi L G0 0008285 negative regulation of cell proliferation cde vi L GO 0017111 nucleoside triphosphatase activity dc 18l O G0 0051301 cell division hok scdc vi 18l scdc 18 Sud N A 1 881 object s jpg A uw 3 4 dv Export Graph List Folder Annotate Current project Public Figure 68 Using a variable query The query results can be saved by clicking the Save button See Section 3 6 Saving the query and creating a smart folder 4 Preparing a BioXM web portal The first three sections have covered the basic steps to get started with the BioXM client software create a data model populate the knowledge base and perform typical queries We will now set up a BIoXM web portal to allow us to execute our query using a familiar Web interface rather than the BioXM client software Instead of using the BioXM query builder and displaying a query in the BioXM interface we can click a hyperlink to run the query and display the query results as a formatted table in a Web browser The BioXM Web Portal Builder has several functions for desig
16. by default in tables option BioRS databank Select the BioRS databank option and EntrezGene from the drop down menu 30 Quick Start General View Items Report Layout f gt BioXM Knowledge Management Environment LX Available view items View items Mapped BioRS entries Object Properties S Name Q Caption Description Object Object type Static type Q Aliases e Shape Creation time Qi Creation user name Qi Last modification time Last modification user name 5 Annotation Assigned annotations QS Number of assigned annotations Qi Assigned annotation attribute t BioRS BMapped BioRS entries Mapped BioRS entry attribute A Net r Knowledge Related objects Number of related objects Qi Relations Relations as graph Q Contexts Name Reports Gene Object EntrezGene Mapped BioRS entries EntrezGene Name EntrezGene 4 Shown by default in tables Sort by default Ascending Sorting nested view item BioRS databank EntrezGene F Use nested view Report mode Always expanded Add Delete Duplicate a iy 2 Variables Name Figure 47 Creating a view View Items tab Mapped BioRS entries definition In the Available view items pa
17. default properties available for the object see Figure 43 Displaying the gene list Initially it is set as the default view however additional views can be created to address specific needs and set as the default view We will create a new view so the gene list displays the information most relevant to this use case 1 To create a new view select Administration gt Views This item will be enabled only for users with the appropriate privileges For more information about privileges see the BioXM User Manual Alternatively in any open view click the Manage button next to the name of the view The Views dialog is displayed 28 Quick Start r gt BioXM Knowledge Management Environment xs Report Default Figure 44 Creating a view the Views dialog Click the New button to display the New View dialog see Figure 45 Creating a view General tab Define the following information for the new view in the General tab Table 6 General tab options Enter Gene list view in the field Allowed types Select the type of object for which the view will be available e g kind Element and element type Gene from the drop down menus Enter a short description of the view optional Select the Public project Allowed for table Select the Allowed for table and Use as default for table options Allowed for report Select the Allowed for rep
18. dialog for specifying the necessary information appears in the right panel 2 We want to search for genes involved in signal transduction so we will perform a search for genes that are classified by the GO ontology entry signal transduction In the Criteria available panel under Object Selection open is an element and select is a gene Click the Add button to list it in the Object to find panel Nothing needs to be changed in the right panel 36 Quick Start gt Find by advanced query BioXM v Define Query Criteria available Object to find Analyze query W Search Results 3 Object Selection BD eee H is the i W Save query 340 Element is a Gene Object Properties 7 Element type i has name H has description Gene H has alias has shape H is created by a user with name is last modified by a user with name has creation time i has last modification time Logical simultaneously alternatively i never Knowledge Network is a target for Functional Classificatic is a source for encoding is related to an object gt is item in container containers operation combine Project Organization gt is owned by Public project is an item in folder BioRS i is mapped to a BioRS entry in Entrez 3 Object Association H is constrained t
19. name Q like GO term to treat them as regular characters 7 Use variable GO term Variable value processing options No special options selected tr Delete aw Overview Variables Object to find is a Gene which is Generate Name T Value dassified by a GO entry which is inferred by ontology entry which has F Auto GO term Pattern Expression signal transduction name like GO term Hee Figure 66 Editing a smart folder query 4 Inthe Variables field click the entry Name and click the Edit button to display the Edit variable dialog Edit Variable Variable name GO term Value signal transduction Figure 67 Adding variables to a query Enter GO term as the variable name and any text in the Value field We will enter signal transduction to set it as the default variable value for the query Click the OK button to define the variable and close the dialog 5 Inthe right panel of the Edit query window select GO term from the drop down menu and click the Apply button 6 Inthe Description field we can enter a description for the query or click the Generate button to generate a description from the query criteria A natural language description of the query is Find all genes which are classified by a GO entry which is inferred by an entry which has a name like any GO term 7 C
20. page to run the Find signal transduction genes query and display the results New pages in the Foswiki system are called topics and are named using a WikiWord A WikiWord is a string containing at least two uppercase letters one of which is the first letter of the word e g NewPage Any such string can be used but we will use the names of our queries as in the BioXM client for simplicity 44 Quick Start Enter the following text to create a heading Queries of interest indicated by the and a page for the query called FindSignalTransductionGenes Queries of interest FindSignalTransductionGenes WebHome edit v Text Settings Help Title WebHome Hi H2 H3 H4 AAA A A Welcome to the Biomax Knowledge Portal I II JULI ai li Iii Base D First time users get a tour introducing the BioXM portal builder WebHomeFirstTimeStart here lt br gt For personal settings change your UserPreferences preferences br Administrators if the data model has changed hit BioxmRefresh Queries of interest FindSignalTransductionGenes wv Save Save and Continue Preview x Cancel Force new revision Figure 71 Editing the WebHome page Click the Save button The edited WebHome page will be displayed amp Biomax Admin Users Log Out The BioXM Knowledge Portal r e You are here BioXM F E ld
21. 4 Click the Next button to continue to the Import Data step of the wizard 24 Quick Start p gt BioXM Knowledge Management Environment Import Table Data Current Step Import Data Details Table parsing errors No table parsing errors occurred Import errors No import errors occurred Processed lines The requested line ranges 100 are processed and accepted Database modifications summary Annotation Basic information 99 object s created Annotation to object assignment 99 object s created BioRS mapping record 99 object s created Element of type Gene 99 object s created Relation of class Functional Classification 666 object s created Revision annotation Basic information 99 object s created Figure 40 Importing data simulating the import The import simulation may take some time but you can continue working with the BioXM system as the import is processed by clicking the Put to background button To display the task again select View Show Background Task Manager in the main menu The Background Task Manager window will be displayed Click the task and the Task Details button to display the task 5 lf there are no problems upon completion of the simulation we can proceed to the actual data import by clicking the Back button See Section 2 5 Completing the import If there are errors reported see Section 2 4 Trouble sh
22. 6 O 0005554 GO 0005643 GO 0 AA SUR F take H m 14 SUR 64595 0 000 S0 742600 000 8 2G O 0016757 GO 0016021 GO 0 A4GALT Homo sapiens P1 PK A14GALT A4GALT 1 PK A4 mu O 0005624 GO 0005795 GO 0 iHomn saniens Poli Figure 32 Importing data choosing the kind of script After the script is defined and saved it will be stored in the database During subsequent data import it can be used by selecting the Existing script option 18 Quick Start 2 2 Configuring the tab import script The next series of steps configures the tab import script used to import the Genes txt data A workflow of several import operations is defined Each import operation is selected from the Available import operations panel on the left The defined workflow is displayed in the Tab import script panel in the middle Depending on the item selected in the middle panel a dialog for specifying the necessary information is displayed in the right panel Note that this kind of three panel layout is often used in the BioXM user interface An option is selected in the left panel listed in the middle panel and defined in the right panel In the following series of steps only the specified options need to be changed other options can be left on the default settings 1 Under Available import operations select Lookup or create element and click the Add button Options for the import operation will be displayed un
23. BioXM Knowledge Management Environment Quick Start BIOXM version 5 0 252 January 2014 Biomax Informatics AG o biomax biomax informatics ag BioXM Knowledge Management Environment Quick Start Biomax Informatics AG BioXM version 5 0 252 Publication date January 2014 Copyright 2014 Biomax Informatics AG Biomax Informatics AG Sitz Martinsried bei M nchen Amtsgericht M nchen HRB 134442 Ust IdNr DE 191 603 142 Steuer Nr 143 100 10945 Vorstand Dr Klaus Heumann Vorsitzender des Aufsichtsrates Prof Dr Hans Werner Mewes Biomax and BioXM are registered trademarks of Biomax Informatics AG in Germany and other countries Registered names trademarks etc used in this document even when not specifically marked as such are not to be considered unprotected by law Table of Contents QUICK Stoico aestu uet tocntdtedaasietice taceo testa tengo ques ese nse eneeaea ce Boece a scena UE eu Rec Ore chau 1 t Designing Ihe Calta MOG Ol T Gentasast a ue ceteeedevienbencasauiel eta a bined 1 flesStanting the BIOXM SYSE seiorn a a a a e T 1 1 2 Displaying the data model 25r a1 eoe hee EAR De ee neYU ades cuM enu ue TE n onk nu h re Bex ATIS RUN R 2 1 5 Addibig elermekib TY OCS credits Sanat ata aetna atee cet Na DAE a Das acu LR E RN RE 2 TA AO GIAG a dqelatiorixclab S erea naa uence nachna cesar tu tascatas mud x URN EE aaa DI d MERI UUE 3 125 AdGING an annotalo Orn eR HL mmm 4 1 6 Mapping BioRS entri
24. Click each option listed in the table below to display the settings in the right panel After selecting the listed settings click the Apply button Table 2 Create annotation operation Tab import script panel Select the element1 option from the drop down menu Create in project Select the Default for Annotation Form radio button The project will be set to the default project for the annotation form i e the Public project Synonyms Set several options Check the Exclude duplicated values check box Check the Add to existing values check box Select the Take from column radio button and B Synonyms from the drop down menu Check the Split with separator check box select the Preset radio button and select the semi colon from the drop down menu Click the Edit link next to Empty invalid values processing A dialog will open Select the Skip radio button for both Empty values and Invalid values and click the OK button The defined operation is shown below gt BioXM Knowledge Management Environment Import Table Data Current Step Define Tab Import Script Stored script Choose Undo Changes New Delete Store Store As Export Import M reon areae ENNNNNNN Available import operations Tab mport script 3 Creation and Lookup of Objects i Synonyms X gt Lookup object by name or alias Lookup oe element amp 1 Lookup or cr
25. GO 0000166 nucleotide binding L3 GO 0000076 DNA replication checkpoint L1 GO 0005737 cytoplasm L3 GO 0000079 regulation of cyclin dependent protein kinase activity L3 GO 0005515 protein binding O GO 0005524 ATP binding L1 GO 0005634 nucleus L3 GO 0006260 DNA replication Sitemap More information Gene list view m O GO 0007049 cell cycle L3 GO 0007067 mitosis L1 GO 0008285 negative regulation of cell proliferation O GO 0017111 nucleoside triphosphatase activity O GO 0051301 cell division To open this object report in the main BioXM client application click Open BioXM Figure 80 Displaying the object report for a gene The current object report for genes simply lists the information defined for the gene list view however we can use a predefined view to display an object report layout designed specifically for the web portal To do this we will first define a new object report view using the BioXM client software 2 Open the BioXM client software and select Administration gt Views to display the Views dialog gt BioXM Knowledge Management Environment il Gene list view Element Gene Figure 81 Displaying the Views dialog in the BioXM client 3 Select the Gene list view and click the Duplicate button The Duplicate view dialog will be displayed 50 Quick Start Duplicate view 3s View Gene list view will be duplicated View
26. Homo sapiens IGCP4 FLJ14797 GCP4 76P TUBGCP4 gam 27229 G0 0000226 GO 00058 15 GO 0000922 G 4 A1BG Homo sapiens A 1B ABG GAB HYST2477 DKFZp686F0970 1 GO 0016020 GO 0005576 5 A28P1 Homo sapiens FOKU HRNEP 1 FOX1 HRNBP 1 A2BP 1 a2bp 84715 60 0000166 60 0003723 60 0005515 G 6 A2M Homo sapiens dkfzp779b086 alpha 2 macroglobulin alph 2 GO 0004867 GO 0005576 GO 0006886 G Hep Bak Next Finis Cancel Figure 41 Importing data choosing a processing policy to perform the import Do the following in this step of the import wizard 1 Click the Allow partial import radio button 2 Clear the Process only lines check box 3 Click the Produce import log check box to record all import operation activity for each line optional 4 Click the Next button to continue to the Import Data step of the wizard The Allow partial import option sets the BioXM system to process the import operations by small portions chunks The system automatically optimizes the number of rows processed based on network capabilities and import speed Partial import allows multiple imports to run simultaneously each allowing one chunk at a time into the queue If the Cancel button is clicked during the import the import is not stopped immediately but after completing the current chunk In addition some import errors are ignored e g Entry not found errors The Allow complete impor
27. OT remarks J Element 4 Element Gene J Element Protein V Ontology entry Z Ontology entry GO V Relation a Saved visualization o J eme Figure 17 Setting what is displayed in the data model graph 2 Click the Select all button or check the Ontology entry GO check box Click the OK button The Ontology entry GO will be displayed in the data model graph 10 Quick Start gt Data Model Graph BioXM BOA Cx Eo TEE nemen E Layout GraphViz directed p E l State model a i3 3 n Annotation Basic information Property name Attribute Synonyms Text Q BioRS entry EntrezGene Attribute ID Text Attribute AllText Text Attribute Chromosome Text Figure 18 Displaying the GO ontology in the data model graph 3 Using the select tool drag the Ontology entry GO to the Element Gene Select Create relation class from Ontology Entry GO to Element Gene from the context sensitive menu The New Relation Class dialog will be displayed P gt BioXM Knowledge Management Environment New Relation Class General Definition Representation Name Functional Classification Description Activate new relation dass Hep ox Cancel Figure 19 Defining a new relation class 4 Inthe General tab enter a name for the relation class
28. The results include 1505 objects genes which are assigned the GO 0007165 signal transduction entry however we actually want a list of all genes involved in signal transduction We will look at the results more closely to see if we have achieved this goal One way to check the results is to open an entry in the GO column e g click GO 0007165 signal transduction to display the detailed report Click the Derived Concepts tab to display all concepts derived from the GO entry To see other entries that may be involved in signal transduction select the Description column enter the term signal transduction and click the Search button GO entries with a description including the term signal transduction are displayed e g GO 0000076 DNA replication checkpoint or GO 0000750 pheromone dependent signal transduction involved in conjugation with cellular fusion We need to refine our search to include such entries Close the GO 0007165 signal transduction window to return to the query wizard G gt GO 0007165 signal transduction Ontology Entry View BioXM e J GO 0007165 signal transduction Report Derived Concepts Relations Graph Annotations View E Ontology entry general information w 5 50 0000076 icati A signal transduction based surveillance mechanism that prevents the initiation of nudear division G0 0000077 INA damage checkpoint signal transduction path
29. ank to check if the entry exists The defined operation is shown below BioXM Knowledge Management Environment es Import Table Data Current Step Define Tab Import Script Stored script Available import operations Tab import script Lookup and assign BioRS entry m 3 63 Creation and Lookup of Objects T Element value Lookup object by name or alias Lookup or create element 3 1 Lookup or create elemeni Selementi Look tol iH Name A Gene Name o E uera 4 B9 Type Gene 5 Use constant value Execute query WJ Create in project Select object 2 Create annotation annotation s d 9 Object Selementi 2 Object Properties p ati Take from column Rename object 8 Name QU Assign description HJ Form 8 Basic information m L4 Aida dieci aias BJ Overwrite Yes iEnirezGene Y 4 Create in project Q Assign sequence Do not trim surrounding spaces QU Assign experimental data Attributes m Assign object shape i 8 B Synonyms V Split with separator i Rename annotation LER d R Annotation and Meta data ee je felemen Preset i x I Create Gun BD Databank EntrezGene IBJ Element name ID Custom Assign annotation T i Lookup annotation uP Element value C EntrezGene ID i Skip lookup by ID Yes CRM l Change annotation Post processing options Edit Qi De
30. art gt BioXM Knowledge Management Environment File Edit View Settings Modeling Administration Search Tools Help a5 a Gene Element Type View iX a Public Repositories General Elements Mff Annotations nz Basic information View E Element general information Manage BioRS entries EntrezGene m eal E UNIPROT_SPROT tome m sa wh an Twe Description Project amp E Protein 15E1 2 Homo sapiens Gene ic zt i wh Onfologies 76P Homo sapiens Gene Public H E GO A1BG Homo sapiens Gene Public fi Queries A2BP1 Homo sapiens Gene poi h Relations A2M Homo sapiens Gene E encoding A2ML1i Homo sapiens Gene Public E Functional Classification A3GALT2 Homo sapiens Gene A4GALT Homo sapiens Q Gene Public A4GNT Homo sapiens Gene Public AAAS Homo sapiens Gene Public AACS Homo sapiens Gene Public AADAC Homo sapiens Gene Public AADACL1 Homo sapiens i Gene Public i AADACL2 Homo sapiens Q Gene Public AADAT Homo sapiens Gene Public AAK1 Homo sapiens Q Gene E Pubic AAMP Homo sapiens Gene Public AANAT Homo sapiens Gene Public AARS Homo sapiens Gene Public AARS2 Homo sapiens Gene Public AARSD1 Homo sap
31. ation annotations Synonyms cdc6 related protein cdc6 cell division cycle 6 homolog s cerevisiae cdc6 cell division cycle 6 s cerevisiae homolog hscdc18 hscdc6 cdc18 cell division cycle 18 s pombe homolog ike cdc6 cdc6 homolog cdc18 hscdc 18 cdc 6 cdc vi cde vi cdc 18l hscdc 6 hscdc vi cdc 181 hscdc 18 cdc 6 hscdc 6 hscdc i HsCDC6 CDC18L HsCDC18 CDC6 To open this object report in the main BioXM client application click Syndicate this site amp 9Rass atom 7 bi 2 Diomax Copyright 1999 2010 by Biomax Informatics AG e Homes hlora og Figure 86 Displaying the predefined object report for a gene 13 The Assigned annotations table can be edited Click the Edit button below the table to edit the annotation Click the Submit button to commit the changes 53 Quick Start Assigned annotations Basic information annotations Synonyms cdc6 related protein cdc6 cell division cycle 6 homolog s cerevisiae cdc6 cell division cycle 6 s cerevisiae homolog hscdc18 hscdc6 cdc18 cell division cycle 18 s pombe homolog like cdc6 cdc6 homolog cdc18l hscdc 18 cdc 6 cdc vi cdc vi cdc 18l hscdc 6 hscdc vi cdc 18l hscdc 18 cdc 6 hscdc 6 hsede vi HsCDC6 CDC18L HsCDC18 CDC6 Submit Cancel Figure 87 Editing the assigned annotation for a gene This concludes the steps for getting started with the BioXM web portal 5 Getting help For more information about using the BioXM Kno
32. bjects in a data model can be easily added deleted edited and visualized The graph viewer allows this editing and extension while enforcing consistency within the data model To display the data model graph complete the following steps 1 Select Modeling Visualize data model in the main menu to display the Visualize data model dialog 2 Select New visualization and click the OK button to display the data model graph P Data Model Graph BioXM amp MEA amp iov PUES Cv S amp amp Layout GraphViz directed D R State m New gt Element type Relation class Context class Ontology Annotation form BioRS databank Experiment method External object type Figure 3 Data model graph with open context sensitive menu 1 3 Adding element types The data model will have two types of elements genes and proteins The properties of the elements are defined by the element type Before adding the data relationships and annotation for the elements we will add the element types to the data model 1 New gt Element type The New element type dialog will be displayed Right click anywhere in the empty field of the data model graph to display a context sensitive menu Select Quick Start gt BioXM Knowledge Management Environment New Element Type General Object Name Definition Representation Extensions Nam
33. button to display the Edit annotation form dialog Quick Start BioXM Knowledge Management Environment Add attribute Figure 11 Adding an attribute to an annotation form Enter a name for the attribute Synonyms and a description optional in the text fields Set the type to be Text Click the Next button 5 Under Attribute value properties check the Multiple values allowed option Click the Finish and the OK buttons to return to the data model graph Q Tip Under Attribute type properties you can also select the Controlled by pattern option and set a pattern i e a regular expression to control the input data 6 Using the select tool assign the annotation form to the gene element by dragging and dropping it onto the gene element type Likewise drag and drop the annotation form onto the protein element type The annotation form is now assigned to the gene element type and the protein element type e Data Model Graph BioXM Em WR m E Ea Layout GraphViz directed State X x J Annotation Basic information Property name Attribute Synonyms Text Element Gene Relation encoding Property name Property description Figure 12 Assigning an annotation form 1 6 Mapping BioRS entries Next we will map the Gene and Protein elements to external database entries integrated
34. crotubule cp4 L G0 0006461 protein complex assembly piv L GO 0007020 microtubule nucleation n4 LJ G0 0008274 gamma tubulin ring complex cp 4 T A1BG Homo sapiens A1B 1 19 L G0 0016020 membrane x L G0 0005575 extracellular region 512477 Zp686F0970 1BG Ipha 1 b glycoprotein gab gene bg b c 16 459 object s E Uu 4d Export Graph List Folder Annotate Current project Public Figure 54 Displaying the Gene list view The appearance of the view is automatically saved for each user and will be the same the next time the view is displayed 35 Quick Start 3 3 Creating a query Next we will create a query to answer a specific scientific question or perform a specific task in our use case In the first example we will create a query to find all signal transduction genes in the knowledge network In the second example we will create a general query to find genes by function Queries can be easily defined within the BioXM system using a graphical user interface which is similar to the import wizard The query builder features a query language similar to a natural language and can support complex search tasks A query can be stored in the query repository for later reuse A query can also be saved as a smart folder within a project folder Each time the smart folder is opened the query is performed ensuring up to date information with no maintenance effort 1 Select Search 9 Find by advanced query in the main
35. d radio button to look entries up by a unique identifier UID Value Set several options e Select the Take from column radio button and D GO Ontology entry Uid from the drop down menu Check the Split with separator check box select the Preset radio button and select the semi colon from the drop down menu Click the Edit link next to Empty invalid values processing A dialog will open Select the Skip radio button for both Empty values and Invalid values and click the OK button The defined operation is shown below amp amp BioXM Knowledge Management Environment mms Import Table Data Current Step Define Tab Import Script Stored script nism en E Creation and Lookup of Objects Lookup object by name or alias a Lookup or create element 2 1 Lookup or create elemeni Selementi e cckup ontology entry BD Name A Gene Name UM Lookup BioRS entry Type Gene E Case insensitive Execute query Hi Create in project Select object 2e mar i Use constant value 2m cs 3 je Selemen Object Properties 3 p Rename object 8 Name Assign description SD Form 85 Basic information J Q Assign object alias i gt ea Yes Take from column Qi Assign sequence ry pne ke Project Assign experimental data D GO Ontology entry Uid E Assign object shape J Synonyms B Synonyms L9
36. defined to restrict the element s use to certain projects by clicking the Add button in the Object Type Scopes dialog and selecting the desired projects in the New Scopes dialog In this use case however all scope capable items should be given the Global Scope setting Basic information to have the Global Scope model e g Project Public Click the Enable Global Scope button After the scope is set click Close to close the dialog window Complete the steps again to set the rest of the scope capable items i e Element Protein and Annotation The scope settings can be displayed in the data model graph by clicking the Toggle scope display button at the top of the window The projects in the scope are displayed for each scope capable item in the data a gt Data Model Graph BioXM amp BOD Qi OEE Greve 83 Layout GraphViz directed v JR n State BioRS entry EntrezGene Attribute ID Text Attribute AllText Text Attribute Chromosome Text Attribute CreationDate Date Attribute Crossreference Reference ihute Curent iN Text Text Attribute Alternative Name Text Attribute Alternative Products Text Figure 23 Displaying scopes in the data model graph Upon defining the scopes the elements and annotation become available in the Repositories folder of the project tree see Figure 16 Object t
37. der Tab import script Click each option listed in the table below to display the settings in the right panel After selecting the listed settings click the Apply button Table 1 Look up or create element operation Option selected in the Settings in right panel Tab import script panel Name Select the Take from column option and A Gene Name from the drop down menu Select the Use constant value option and Gene from the drop down menu Create in project Select the Default for Element Type radio button The project will be set to the default for Gene elements i e the Public project The defined operation is shown below E gt BioXM Knowledge Management Environment Import Table Data Current Step Define Tab Import Script Stored script Available import operations Tab import script Lookup or create element C Creation and Lookup of Objects j i Name Qi Lookup object by name or alias aaa lookup or create element 3 9 saree or create allt LName AzGeneName o O Gene Name Qi Lookup ontology entry n Name l Q Lookup BioRS entry m Gene E Case insensitive QV Lookup external object J f reate in proje Pry Use constant value Qi Select object Object Properties Rename object Assign description Q Assign object alias i Assign sequence A Gene Name v Qi Assign experimental data Take from column
38. e Gene Description Activate new element type Heb Figure 4 Adding a new element type 2 Enter the name e g Gene in the field We will use the default settings for the other tabs Object Name Definition used to set the element name to be controlled by a certain pattern Representation used to define how the element appears in the interface and Extensions used to set extensions for the element type Click OK The Gene element type will appear in the data model graph 3 Complete the steps again to add a protein element type Instead of Gene enter Protein in the Name field The Protein element type will appear in the data model graph P Data Model Graph BioXM o B 2S RAC Qmm WH Creme E a ee Layout GraphViz directed v R State m E x Element Gene Element Protein Property name Property name Property description Property description Figure 5 Data model graph with elements 1 4 Adding a relation class To create the relationship between genes and proteins in the data model we will add a relation class to define the relationship between the gene element type and protein element type 1 Using the select tool l in the upper left corner add a relation class by dragging and dropping one element onto another For our use case drag the Gene element type to the Protein element type 2 Select Create rela
39. e Annotation form check box and select Basic information from the drop down menu Click the Apply button 51 Quick Start G gt BioXM Knowledge Management Environment Edit View General View Items Report Layout Available view items Assigned annotations Object Properties Reports t Name Obiect Name Assigned annotations Basic information anno Caption RUE Mapped BioRS entries Mapped BioRS entry att Related objects GO en Assigned annotation Assigned annotations Shown by default in tables Sort by default Ascending Sorting nested view item Qi Creation user name F E Last modification time v Annotation form Gi Last modification user name e ENTUM i Number of assigned annotations F All revisions G Assigned annotation attribute o BioRS Mapped BioRS entries Use nested view Mapped BioRS entry attribute Knowledge Network Qi Related objects Q Number of related objects Relations Always expanded tQ Relations as graph 4 Report mode Figure 84 Adding assigned annotation in the object report view 10 Click the Report Layout tab to open it Select the Predefined radio button and select Portal view from the drop down menu n gt BioXM Knowledge Management Environment T Edit View Ge
40. e Text Attribute Evidence Text Pirbuln Frasi Tied Attribute FtDescription Text Atribute Remark Text Attribute FtKey_count Text Firbui RGD Ted Attribute FtKey Text Pitribute Satus Tert Attribute FtLength Integer Attribute Update Date Attribute Function Text Attribute Variants Integer Attribute Gene Text Attribute Taxonomy Text Attribute Genome_DB Text Attribute Genelvodel Text Attribute Induction Text Attribute ReferencelD Text Attribute InterPro DB Text Attribute Journallssue Integer Figure 15 BioRS databanks in the data model The BioRS databanks have been added to the data model Additionally the BioRS databanks are available in the BIoRS entries repository in the project tree of the BioXM client In fact all object types configured in the data model graph are available under Repositories in the project tree As the objects are configured and their scopes are defined the repositories corresponding to the object types become available automatically Note that the graphic below shows the project tree for the finished data model In the current step only the BioRS entries and Ontologies repositories are shown Other repositories will be added after defining the scopes biomax Public BE Public E M Repositories ih Annotations i Basic information ih BioRS entries pU EntrezGene E E UNIPROT SPROT E M Elements ih Ontolog
41. e 15 le 11object s m P amp Export Graph Figure 59 Creating a query checking the results 38 Quick Start 3 5 Redefining the query We will redefine the query to include all entries which are assigned the GO 0007165 signal transduction classification or are inferred from such entries 1 Click the Back button to redefine the query 2 Inthe Object to find panel click the has name criteria to select it and click the Delete button Click Yes in the dialog to confirm the deletion 3 Inthe Criteria available panel under Knowledge Network select is inferred by ontology entry which and click the Add gt gt button to list it in the Object to find panel 4 Inthe Criteria available panel under Object properties select has name and click the Add gt gt button to list it in the Object to find panel Enter signal transduction in the Pattern field in the right panel and click the Apply button 65 gt Find by advanced query BioXM pore a opammi aae amry W Search Results is a Gene which is dassified by a GO entry which w Save query Q is inferred by ontology entry which signal transduction QS has name o CEEE uses T aw on NOT and parentheses for matching against logical expressions Use to match any character and for any number of characters Use quotes t
42. e data model This mapping process between the defined data model and the input data ensures consistency in the knowledge network This section describes importing a table of gene data creating an import script and saving it for future use An import wizard guides the configuration of the import script It includes specifying how the data is imported assigning annotation external databank entries and ontology entries to the elements and looking up and creating relations 2 1 Defining the import To import the table Genes txt we will use the Tabular data import function which allows us to specify how data will be uploaded according to the data model In the following series of steps only the specified options need to be changed other options can be left on the default settings 1 Select File gt Import Table in the main menu to display the first step of the Import Table Data wizard import wizard 2 Dothe following to choose the data source 1 Enter the path to the file to be used for import Alternatively browse to the location of the file to upload 2 Select the type of file for import e g the Autodetect option to detect the format automatically 3 Click the Next button to continue to the Define Physical Layout step of the import wizard gt BioXM Knowledge Management Environment X Import Table Data Current Step Choose Data Source File File name bioxm_workshop Workshop Workshop Genes
43. e g Functional Classification In the Definition tab enter a forward name e g classifies and a backward name e g is classified by in the fields Click OK to close the dialog The GO ontology will be related to the Gene element type 1 8 Defining object type scopes Next we will define the scopes for the object types Scopes allow semantic objects of a specific class or type to be restricted to a defined set of projects i e the object type scope defines the project s in which the object type can be used The Global Scope setting allows the object type scope to be set to all projects Objects based on object types with the Global Scope setting can be created within any project including any new projects that may be created Special assignments e g annotation assignments BioRS databanks and ontologies are not scope capable but are considered to have the Global Scope setting That is they can be used in all projects Elements such as Gene and Protein relations and annotations on the other hand are scope capable and can be restricted to certain projects In this use case however they will be given the Global Scope setting 1 Inthe data model graph right click an element e g Element Gene and select Scopes from the context sensitive menu 11 2 Quick Start gt Data Model Graph BioXM e Align 100 Layout Graphiiz directed v 8 Annotation Basic inf
44. eate element elementi gt Name A Gene Name Lookup ontology entry w Lookup npa AR 87 Type Gene a Lookup external object e can a rig ini gt Execute query A den 7 Exdude duplicated values Select object MJ Object Selementi Object Properties v ors M V Add to existing values B eme died 8 Form 8 Basic information tQ Assign description Assign object alias Assign sequence Assign experimental data Q Assign object shape Rename annotation Annotation and Meta data B Synonyms E Assign annotation 7 Use constant value Take from column E Do not trim surroundi ces Lookup annotation gods EHE Change annotation v 7 Split with separator Show description Add gt gt Add Delete a iv Apply Discard Overview Variables Name Type Value Add Data preview Click a column to select it A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid 2 15E1 2 Homo sapiens MGC 129938 15E1 2 MGC 129938 15e1 2 283459 GO 0017068 GO 0000004 GO 0005554 G 76P Homo sapiens GCP4 FLJ14797 GCP4 76P TUBGCP4 gam PAZZ G0 0000226 GO 0005815 GO 0000922 G B a d a snc Deum mmm ml ain a ma na alae an aaa le 0 0037020 00 000n0nn A C0 0 r rr Ac L Help Bak Next gt Finish Cancel Figure 34 Importing data tab import script Create annotation
45. ent General View Items Report Layout Available view items View items Related objects g e Object Properties a Reports 8 Description EntrezGene Mapped BioRS entries EntrezGene Object Chromosome Mapped BioRS entry attribute Chromosome 4 Shown by default in tables Synonyms Assigned annotation attribute Synonyms Q Object type Sort by default Ascending _ Static type Related objects Related objects i Aliases Sorting nested view item Shape gt Creation time Creation user name i Qi Last modification time Related object is Last modification user name 23 69 Annotation Q Assigned annotations Target Number of assigned annotations QU Assigned annotation attribute Q Source or target C 9 BioRS gt Mapped BioRS entries E v Relation dass n n Source Qi Mapped BioRS entry attribute Knowledge Network g Jate objects A D A a O E LM Q Number of related objects v Related object type Qi Relations Q Relations as graph Kind Qi Contexts Ontology entry Qi Contexts as graph S Project Organization Ontology Project Search l B Li L2 h On ese raculte Variables ene Type Value NT Edit Delete C9 Com Figure 50 Creating a view Vie
46. es ssssssssssssssssssssssessese ee se eme ee enses sisse se se sensere nnns 6 Les ASSOCIANO AN OMOlOOY xedienii mud ca ctu rura tete s enun Ee ure bleue upn E tra A ERUEBE TurerHBE Rue 10 1 8 Defining object YPE SCODOS a5 acetic Do Ee e Pe o E buc Ree rs ER t tus m paese un rd 11 129 D ennindgrelauoh elass SCODSS usu iueatue da ns lle setae elas lores aaa TUM DEOS 14 1 10 Saving the data model layout ccc ccc ccc e cece cece e tent eee sese ee ne nennen 15 1 11 Displaying a saved data model layout cccc cece eee e eee eeeeeeeeaeeeseseeeaeeuseeaeeanenaenas 15 2 IDOL dala aeaa uice Ru Ree Du e na LO nc omanausowe a sconces cen E IU DUM DER TR LANE DUE 17 2 fea BY lal alo Me a oo gm REOR 17 2 2 Configuring the tab import script cc ccc cee ce cece cece eee ee eee eee mem me me ne nennen nnns 19 2 3 OMAN are IDOL ss custexsosicsens aate rue an aaae r a ser azer eects stacker 24 2 4 Ttoublesshootg INE IRTDOPU coeunt rete epit stad eni De pn Hen basic ED OE mede Loupe e aa Med pae de 25 2 5 COMPETING INE MOON m rc 26 3 Preparing views and queries 42 2 2 22220006 dc ncteecacteeseiecaacsccceedaeutoecacsheedeucbaicedecdesasedsacdeasceacadeeenass 28 cM ER UTC antes UT 28 3 2 DISDIAVIING Ihe VIEW casco he oEu E a Foch a tas mu aEecb mate a a Farb ace ve nnL NC DUERME nS Pur PULS 35 Dude Greaing a GUEN MN TP ERRRRRR 36 3 4 Displaying the query resul
47. es option P amp BioXM Knowledge Management Environment New View General View Items Report Layout Available view items View items Object m Object Properties Mas arene gt Name Name Gene 69 Caption Gene Cees a O Object Description V Shown by default in tables Z JObject Object type 7 Sort by default Ascending H Aliases Sorting nested view item Creation user name Last modification time F Use nested view Qi Last modification user name 5 6 Annotation Qi Assigned annotations gt Number of assigned annotations Report mode Assigned annotation attribute BioRS Always expanded Q Mapped BioRS entries Mapped BioRS entry attribute e eisai Knowledge Qi Related objects QS Number of related objects gt Relations Qi Relations as graph Q Contexts Show description Add gt gt Delete Duplicate a w Figure 46 Creating a view View Items tab Object definition In the Available view items panel under BioRS select the BioRS mapped BioRS entries option and click the Add button Define the following information in the panel on the right and click the Apply button Table 8 View Items tab Mapped BioRS entries definition Enter EntrezGene in the field Shown by default in tables Select the Shown
48. folder will be created in the Public project and is accessible using the project tree see Figure 63 Selecting a smart folder in the project tree 3 Editing the smart folder Next we will make a more general query that can handle variables This will allow us to perform more flexible queries to find genes by function in general i e genes related to any GO terms not only signal transduction The general query is similar to the Find signal transduction genes query so we can simply duplicate that query and edit it 1 Inthe project tree select the Find signal transduction genes smart folder Right click the smart folder and select Duplicate folder 40 Quick Start gt BioXM Knowledge Management Environment IIT File Edit View Settings Modeling Administration Search Tools Help amp biomax Public 3 Find signal transduction genes Q Public S L My queries e Report Results Results Graph Annotations Repositories z z s SMA Annotations Open in new window fi Gene list view m E Basic information Cut Ctrl X Gf BioRS entries Copy Ctrl C z Search H Elements Past Cul V r2 3 Ontologies e T Gene Synonyms EntrezGene Chromosome GO t iM Queries Remove from Folder DC6 Homo sapiens dc6 related protein 990 7 3 GO 0007089 traversing sta EM Relations Delete meni cyde 6 h
49. hViz directed n Annotation Basic information Property name Attribute Synonyms Text Project Public Ontology entry GO Property name Property description Property UID Relation rey tat Q Element Gene Element Protein Relation encoding Property name a Property name Property description Property description Project Public Project Public Annotati o BioRS entry EntrezGene P BioRS entry UNIPROT SPROT Attribute D Text Attribute AllText Text Attribute AllText Text Attribute _ID_ Text Attribute Chromosome Text Attribute AccNumber Text Attribute CreationDate Date Attribute Allergen Text Attribute Crossreference Reference Attribute Alternative Name Text Attribute CurrentID Text Attribute Atemative Products Text Attribute Description Text ibute Authors Author Mtriburtea Distashnalans Taxt Figure 29 Displaying a saved layout in the data model graph 16 Quick Start 2 Importing data Now that we have the basic data model established we will populate the knowledge network with data and information from external resources The BioXM system has a versatile importer for tables of data which enables users to define the semantic of the table columns and graphically build instruction sets scripts to guide the data import During the import information contained in the input data file is transformed according to the semantics of th
50. i cdc 181 hscdc 18 cdc 6 hscdc 6 hscdc vi HsCDC6 CDC18L HsCDC18 CDC6 CDT1 Homo cdt i 81620 16 1 G0 0005634 nucleus sapiens double parked drosophila homolog of 3 GO 0000076 DNA replication checkpoint cdt 1 O G0 0003677 DNA binding dna replication factor 3 G0 0005515 protein binding dup L3 G0 0005657 replication fork chromatin licensing and dna replication factor 1 O GO 0006260 DNA replication ris2 1 G0 0007049 cell cycle the dup protein G0 0030174 regulation of DNA dependent DNA replication initiation cdt 1 cdti the dup gene cdt1 e Figure 74 Displaying the FindSignalTransductionGenes query The same steps can be used to add the second query Find genes by function 1 Open the WebHome page and click the Edit tool Edit the page to create a new page called FindGenesByFunction for the query 46 Quick Start WebHome edit v Text Settings Help Title WebHome Vll Wii il i Il iii xm pi Hi H H3 H A AAA FA vo Welcome to the Biomax Knowledge Portal First time users get a tour introducing the BioXM portal builder WebHomeFirstTimeStart here br For personal settings change your UserPreferences preferences br Administrators if the data model has changed hit BioxmRefresh Queries of interest FindSignalTransductionGenes FindGenesByFunction w Save H Save and Continue Preview x Cancel F
51. iens Gene pe AASDH Homo sapiens Gene AASDHPPT Homo sapiens Gene pase AASS Homo sapiens Gene E AATF Homo sapiens Gene Public AATK Homo sapiens Gene Public ABAT Homo sapiens Gene Public ABC1 Homo sapiens Gene Public ABCA1 Homo sapiens Gene Public ABCA 12 Homo sapiens Gene Public ABCA 13 Homo sapiens Gene Public a 16 459 object s z amp 1 He Export Graph Folder Current project Public Figure 43 Displaying the gene list The Element general information view is the built in default view for genes In Section 3 1 Creating a view we will create a view for genes which is tailored for use in the gene index use case 3 Preparing views and queries In this section we will prepare the system for use by creating views queries and smart folders This will allow us to tailor how the information in the gene index knowledge network is presented so we can query the knowledge network explore the network graph and report the query results as specifically needed We will create a gene list view and smart folders tailored to our use case 3 1 Creating a view Views display a selection of information about selected objects Information displayed in the view can be taken from the object properties such as name and description or from other associated objects For each element there is always one built in view e g Element general information which shows the
52. ies plo fi Queries S Relations be Functional Classification Figure 16 Object types of the data model in the project tree Quick Start 1 7 Associating an ontology Next we will add an ontology to the data model Ontologies a central concept in knowledge management relate the conceptualization of a domain to the data model Ontologies are often developed by domain experts as a set of scientific nomenclature and are widely used in the sciences We will associate the GO ontology with the Gene elements The GO ontology has already been imported into the BioXM system and is available in the project tree in the Ontologies repository of the project tree see Figure 16 Object types of the data model in the project tree We only need to associate the ontology with the Gene elements For more information about importing an ontology see the BioXM User Manual 1 If the Ontology entry GO is not already displayed in the data model graph it needs to be displayed From the main menu select Modeling Visualize Data Model to display the Visualize Data Model dialog A j BioXM Knowledge Management Environment OS Visualize Data Model Select All Deselect All 4 Annotation Z Annotation Basic information V BioRS entry Z BioRS entry EntrezGene 7 BioRS entry UNIPROT_SPROT BioRS entry UNIPROT_SPROT features n BioRS entry UNIPROT_SPROT references BioRS entry UNIPROT_SPR
53. ioXM Le jme 3 an amp ove amp Es Se navga H a amp Layout GraphViz directed v GES l State x New gt Element type Relation class Select All Ctrl A Context class i X Noe Ctrl Shift A ontext class Create new annotation form f Ontology Invert Selection Ctrl R z Enter new annotation form name Annotation form E Basic information BioRS databank Experiment method External object type Figure 8 Adding a new annotation form to the data model 2 4 Quick Start Enter a name e g Basic information for the new annotation form in the field and click OK The Annotation Basic information form will be displayed in the data model graph gt Data Model Graph BioXM Align 100 A Ee e Navigator 8B Layout GraphViz directed p l State E x Element Gene Relation encoding Property name gt Property description Figure 9 New annotation form in the data model Right click the Annotation Basic information form and select Edif from the menu to display the Edit annotation form dialog j BioXM Knowledge Management Environment Edit annotation form Basic information No attribute is selected cat Remove Use example value as default Figure 10 Editing an annotation form In the Attributes section click the Add
54. ject report in the web portal Information about each gene can be displayed in an object report by clicking the hyperlink in the Gene column Like any other view object reports can be tailored to display particular information Next we will display an object report and use a predefined view tailored for use in the BioXM web portal We will modify the view to allow the object report to be annotated directly in the web portal 1 To display information about a particular gene click the hyperlink e g CDC6 Homo sapiens in the Gene column of the gene list view The object report for the gene will be displayed 49 Quick Start t T 8 ObjectReport BioXM Foswiki Mozilla Firefox eas G ObjectReport BioXM Foswii The BioXM Knowledge Portal e You are here BioXM ObjectReport Pd G o E B f biomax biomax informatics ag Report Home Gene CDC6 Homo sapiens Synonyms cdc6 related protein cdc6 cell division cycle 6 homolog s cerevisiae cdc6 cell division cycle 6 s cerevisiae homolog hscdc18 hscdc6 cdc18 cell division cycle 18 s pombe homolog like cdc6 cdc6 homolog cdc18l hscdc 18 cdc 6 cdc vi cde vi cdc 18l hscdc 6 hscdc vi cde 18l hscdc 18 cdc 6 hscdc 6 hscdc i HsCDC6 CDC18L HsCDC18 CDC6 EntrezGene 990 Chromosome 17 GO L1 GO 0007089 traversing start control point of mitotic cell cycle G0 0008156 negative regulation of DNA replication L1
55. lder Duplicate query Query Find signal transduction genes will be duplicated Query name Find genes by function Figure 64 Duplicating a smart folder 2 Inthe project tree select the Find genes by function smart folder Right click the smart folder and select Edit smart folder to display the Edit query dialog gt BioXM Knowledge Management Environment Erma File Edit View Settings Modeling Administration Search Tools Help amp biomax Public J Find genes by function Qj Public S O My queries eap 5 8 Find signal i oah aic Open in new window view Ifl remm 5 i 2 Cut Ctrl X g jotations E Basic informatic Copy Ctrl C Gene a Search E h BioRS entries Paste Ctrl V E 3 Elements Gene Synonyms EntrezGene Chromosome GO tg E W Ontologies Panove hom AS CDC Homo sapiens dc6 related protein 990 5 60 0007089 traversing sta WA Queries Delete ae s O G0 0008156 negative regu EM Relations Bebes L G0 0000168 nucleotide bi Edit Properties ivisi isi encoding aimans Eo a cyte 6 core A G0 0000076 DNA replicati E Functional Clas Edit smart folder L3 G0 0005737 cytoplasm Edit variables scdc6 D GO 0000079 requlation of E c18 cell division cyde 18 s pombe LI GO 0005515 protein bindi Edit local views jomolog ike L G0 0005524 ATP binding
56. lick the OK button to close the Edit query window and display the Find genes by function results tab 8 Click the Show Query Variables button to display the GO term variable field Use signal transduction or enter another GO term in the field and click the Apply button The query results will be displayed in the table 42 Quick Start BioXM Knowledge Management Environment File Edit View Settings Modeling Administration Search Tools Help biomax Public Fa Fi a d X Find genes by function x 3 3 My queries 589 Report Results Results Graph Annotations Find signal trans Repositories Annotations Show Query Variable App Revert Save Cancel E Basic information S BioRS entries EntrezGene Overview E UNIPROT_SPROT Object to find is a Gene which is classified by a GO entry which is inferred by ontology entry which has name like GO term Wh Elements E Gene Variables Protein Ontologies GO term signal transduction GO WA Queries ih Relations E encoding Functional Classifica view E Gene list view Manage oes E E Gea Gene Synonyms EntrezGene GO ES CDC8 Homo sapiens cdc6 related protein 990 17 G0 0007088 traversing start control point of mitotic ce spinis cyde 6 homolog Q 60 0008156 negative requlation of DNA replication LM L GO 0000166 nucleotide
57. ment Element Gene Relation encoding X Property name Property description m BioRS dat mapping BioRS dat mapping BioRS entry UNIPROT SPROT Q BioRS entry EntrezGene Attribute AllText Text Attribute _ID_ Text Attribute _ID_ Text Attribute AllText Text Attribute Acc Number Text Attribute Chromosome Text Attribute Allergen Text Attribute CreationDate Date Attribute Altemative Name Text Attribute Crossreference Reference Attribute Alternative Products Text Attribute CurrentID Text Attribute Authors Author Attribute Description Text Attribute Biotechnology Text Attribute Discontinue Date Date Attribute CatalyticActivity Text Attribute Disease Text Attribute Caution Text Pitribute rum Text Attribute CellularLocation Text Tm Birkufa arema Text Atribute CoFactor Text Attribute Gene Text Attribute Crossreference Reference Attribute GeneType Text Atribute Database Text Piiributa GO TE Attribute Description Text donned HONG Text Attribute DevelopmentalStage Text Attribute HPRD Text Attribute Disease DB Text Attribute Interaction Text Attribute Disease Text Pitribute KEGG Text Attribute Domain Text Attribute Literature Text Attribute ECnumber Text Attribute Location Text Attribute Entry Date Date Attribute Organism Text Attribute Entry Name Text Attribute Pathway Text Attribute Enzyme Regulation Text Attribute PreferredGen
58. menu 7 BioXM Knowledge Management Environment File Edit View Settings Modeling Administration Tools Help R 7 i Basic information BioRS entries e EntrezGene 3 z UNIPROT SPROT Elements 3 ocg Gene ih Edit Query Templates Tew Ll view Protein k 223153 12 a Go 15e1 2 li Queries hypothetical protein loc283459 Mh Relations mgc 129938 5 encoding gc 129938 E Functional Classification potete protein loc 283459 ypothetical protein loc 283459 mac 129938 1BG Homo sapiens Tp o1 19 G GAB YST2477 Zp686F0970 ress lpha 1 b glycoprotein vni gab gene g ab fzp686f0970 ibg yst2477 a 1b glycoprotein se gab protein ib a ibg ax 1b glycoprotein yst 2477 a 1 b glycoprotein dkfzp686f 0970 dkfzp686f 0970 a ib abes yst 2477 AAAS Homo sapiens A A 5056 12 AAASb GLOO3 JADRACALA JADP ACALIN l L L a 16 459 object s aw SEE YF r Export Graph List Folder Current project Public Figure 55 Creating a query accessing the query wizard The Find by advanced query wizard will be displayed It is similar to the import wizard with three panels Query criteria are selected from the Criteria available panel on the left The added criteria are displayed in the Object to find panel in the middle Depending on the criteria selected in the middle panel a
59. ms Text Q Element Gene Relation encoding Q Element Protein Property name Property name PR Create relation class from BioRSEntry EntrezGene to Element Gene Create relation class from Element Gene to BioRSEntry EntrezGene Create relation configuration from BioRSEntry EntrezGene to Element Gene Create relation configuration from Element Gene to BioRSEntry EntrezGene ni Assign Element Gene to BioRS databank EntrezGene BioRS Cancel Figure 14 Assigning an element to a BioRS databank An assignment is created between the two Assignments differ from relations as follows Assignments are preferred if using a data set as the basis of an object definition extra information cannot be added Assignments are indicated by italic text in the data model graph Relations are semantic relationships extra information can be added using annotation forms To add the UNIPROT SPROT databank and assign the protein element type to it complete the steps again In Step 3 select the UNIPROT SPROT BioRS databank In Step 5 drag the BioRS entry UNIPROT _SPROT to the Element Protein Quick Start 4 Data Model Graph BioXM A non fee EJEN nanata E iJ e amp Layout GraphViz directed v b RI l State i XX J Annotation Basic information Property name Attribute Synonyms Text Annotation assignment Annotati sign
60. name Object report view Figure 82 Displaying the object report for a gene 4 Enter anew name e g Object report view for the view in the dialog field Click the OK button The Views dialog will be displayed again 5 Select the Object report view and click the Edit button to display the Edit view window P gt BioXM Knowledge Management Environment General View Items Report Layout Name Object report view Allowed type s All types Object type Project H3 Public Allowed for table 7 Allowed for report Use as default for table V Use as default for report Load table rows incrementally F For nested reports only c cance Figure 83 Defining the object report view 6 Inthe General tab remove the check from the Allowed for table check box so the view applies to single objects only not to tables of objects 7 Click the View items tab to open it Instead of only showing the Synonyms assigned annotation attribute we will display the assigned annotation form This allows the annotation to be edited in both the BioXM client software and the BioXM web portal 8 In middle panel under View items select Synonyms and click the Delete button Click Yes to confirm the deletion 9 Inthe Available view items panel on the left under Annotation select Assigned annotation and click the Add button In the right panel select th
61. nel under BioRS select the mapped BioRS entry attribute option and click the Add button Define the following information in the panel on the right and click the Apply button Table 9 View Items tab Mapped BioRS entry attribute definition Name Shown by default in tables Databank Attribute Enter Chromosome in the field Select the Shown by default in tables option Select EntrezGene from the drop down menu Select Chromosome from the drop down menu 31 Quick Start p BioXM Knowledge Management Environment General View Items Report Layout S Object Properties Name Reports E ncn iB Gene Object Name Chromosome L Description EntrezGene Mapped BioRS entries EntrezGene E SS Object gt Object type E Sort by default Ascending Static type Aliases _ Shape Databank Q Creation time EntrezGene X Creation user name Last modification time Attribute Last modification user name Chromosome 2 3 Annotation QU Assigned annotations Qi Assigned annotation attribute 2 69 BioRS Mapped BioRS entries Q Number of assigned annotations Show attribute value Show SearchTool hyperlink Show hyperlink based on template Q9 IMapped BioRS entry attribute Knowledge Network Related objects gt Number of related objects e Relations Use Gvalue amp inside the URL pattern Qi Relations as gra
62. neral view Items Report Layout Default Pie Histogram for Object Report Use layout for table report exclusively optionally eb Figure 85 Selecting the predefined layout for the object report view 11 Click the OK button to close the Edit view window Click Close to close the Views window 12 We can now return to the BioXM web portal Reload the gene object report to show the new object report layout 52 Quick Start amp Biomax Admin Users Log Out The BioXM Knowledge Portal Search c You are here BioXM ObjectReport Pd e 9E g Q9 amp biomax biomax informatics ag Report Home CDC6 Homo sapiens Gene CDC6 Homo sapiens More information EntrezGene 990 Gene list view Chromosome 17 Object report view GO D GO 0007089 traversing start control point of mitotic cell cycle O G0 0008156 negative regulation of DNA replication 1 GO 0000166 nucleotide binding 0 GO 0000076 DNA replication checkpoint 1 G0 0005737 cytoplasm 1 G0 0000079 regulation of cyclin dependent protein kinase activity 1 G0 0005515 protein binding 1 G0 0005524 ATP binding O G0 0005634 nucleus 1 GO 0006260 DNA replication 16G0 0007049 cell cycle 1 GO 0007067 mitosis 1 G0 0008285 negative regulation of cell proliferation n GO 0017111 nucleoside triphosphatase activity 1 G0 0051301 cell division j Assigned annotations Basic inform
63. nesByFunction i oe e L LLLI vi Tull i Tull P Mdh hull f Hi H2H3H4 A A AA A E Find genes by function SBIOXM QUERY query Find genes by function 4 Main BiomaxAdmin 11 Mar 2011 vw Save B Save and Continue 5 Preview 3 Cancel F Force new revision Figure 77 Editing the FindGenesByFunction page The FindGenesByFunction page will be displayed with a field for entering any GO term amp Biomax Admin Users Log Out The BioXM Knowledge Portal i You are here BioXM FindGenesByFunction 6 E o amp g Q9 amp P a biomax E Find genes by function Home Find genes by function Object to find is a Gene which is classified by a GO entry which is inferred by ontology entry which has name like GO term Sitema j GO term signal transduction BiomaxAdmin 11 Mar 2011 Figure 78 Displaying the FindGenesByFunction page Use the default term signal transduction or enter any other GO term and click the Search button The query results will be displayed 48 Quick Start The BioXM Knowledge Portal amp Biomax Admin Users Log Out f gt biomax mE biomax informatics ag You are here BioXM FindGenesByFunction Find genes by function 1881 items found 96440 l EdGO e Home Gene Rows 25 Page 1 976 Prev Next Sitemap CDC6 Homo sapiens cdc6 related protein 990 17 1 G0 0007089 traversing start c
64. ning a BioXM Web interface for a specific project e g customizing reports and query forms making reports editable defining dynamic thesauri and setting up specific workflows and wizards but we will focus on using the portal to run our queries and display the results Tip We will cover the basic steps for using the BioXM web portal here More information about the BioXM Web Portal Builder can be found on the BioXM Support Web nttps ssl biomax de info biomax bin view BioXM PortalBuilder A working knowledge of HyperText Markup Language HTML and Foswiki is helpful http foswiki org System WebHome provides numerous Foswiki materials 4 1 Logging into a BioXM web portal To login into a BIoXM web portal complete the following steps 1 Open a browser and enter the URL for the BioXM web portal login window The login page will be displayed 2 Enter you user name and password Click the Login button The BioXM web portal entry page will be displayed 43 Quick Start amp Biomax Admin Users Log Out The BioXM Knowledge Portal e You are here BioXM PA AzZzaEaOB ie biomax gt biomax informatics ag Welcome to the Biomax Knowledge Portal First time users get a tour introducing the BioXM portal builder here For personal settings change your preferences Administrators if the data model has changed hit BioxmRefresh Home Sitemap er m K biomax Figure 69 Opening the BioXM web por
65. o have the number o is in results of a query which i is in results of a query based on t 3 Annotation H has of Synonyms assigned annot n p Add gt gt tr Delete a Vv Figure 56 Creating a query Find by advanced query wizard 3 Inthe Criteria available panel under Knowledge Network open is related to an object and select is classified by a GO entry Click the Add button to list it in the Object to find panel 4 Inthe Criteria available panel under Object properties select has name Click the Add gt gt button to list it in the Object to find panel Enter signal transduction in the Pattern field in the right panel and click the Apply button 6 gt Find by advanced query BioXM 5 has name signal transduction o E l Use amp T or AND OR NOT and parentheses for matching against logical expressions Use to match any character and for any number of characters Use quotes to include spaces into patterns Prepend a before special characters to treat them as regular characters Figure 57 Creating a query defining criteria A natural language description of the query is Find all objects which are genes which are classified by a GO entry like signal transduction 3 4 Displaying the query res
66. o include spaces into patterns Prepend a before special characters to treat them as regular characters Figure 60 Creating a query redefining criteria A natural language description of the query is Find all objects which are genes which are classified by a GO entry that is inferred by an entry like signal transduction 5 Click the Next gt button to display the query results E gt Find by advanced query BioXM C 60 0007089 traversing start control point yc L GO 0008156 negative regulation of DNA r omolog s cerevisiae G0 0000166 nucleotide bindin L L L nsi eTA o dz GO 0000078 DNA replication checkpoint erevisiae homolog heic L GO 0005737 cytoplasm scdc6 GO 0000079 regulation of cyclin dependa cdc18 cell division cyde 18 L GO 0005515 protein binding s pombe homolog ike O 60 0005524 ATP binding cdc6 O G0 0005634 nucleus prem G0 0006260 DNA replication EI 0 G0 0007049 cell cycle cdc 6 L GO 0007067 mitosis cdc vi L GO 0008285 negative regulation of cell pt kdc vi O 60 0017111 nucleoside triphosphatase dc 18l 3 GO 0051301 cell division ET HsCDC6 CDT1 Homo sapiercdti 81620 16 GO 0005634 nucleus ouble parked drosophila 3 60 0000076 DNA replication checkpoint peer 0 G0 0003677 DNA binding kina replication factor dcm 5 protein binding E 1 881 object s E
67. omolog s O 60 0008156 negative regu E encoding e 7 O G0 0000166 nucleotide bi E Functional Classification Edit Properties c6 cell division cyde 6 s cerevisiae 1 G0 0000076 DNA replicati Edit smart folder O G0 0005737 cytoplasm Edit variables scdc6 LI GO 0000079 requlation of i c18 cell division cyde 18 s pombe L1 GO 0005515 protein bindi imc omolog ike A G0 0005524 ATP binding Duplicate ins i 1 60 0005634 nucleus homolog rm s iean Create query template cial L GO 0006260 DNA replicatiq E AIC cll oo QN scdc 18 LJ GO 0007049 cell cycle kdc 6 LI GO 0007067 mitosis kede vi i GO 0008285 negative requ kdc vi L G0 0017111 nucleoside tri c 18l L3 60 0051301 cell division scdc 6 scdc vi 18l scdc 18 6 scdc 6 scdc vi sCDC6 CDT Homo sapiens pdt 81620 16 L1 G0 0005634 nucleus ea parked drosophila homolog of O G0 0000076 DNA replicatic kdt D s inei GO 0003677 DNA binding oo m O 60 0005515 protein bindi omat n licensing and dna replication L3 G0 0005657 replication fo 1 O 60 0006260 DNA replicati is2 O G0 0007049 cell cycle dup protein L G0 0030174 regulation of kdt 1 ti dup gene dti omatin licensing and dna replication 1 881 object s a wu OD C Export Graph List Folder Annotate Smart folder Find signal transduction genes Current project Public Figure 63 Selecting a smart folder in the project tree Enter Find genes by function to rename the smart fo
68. on time Qi Creation user name Last modification time Annotation form Last modification user name 6 Annotation Basic information Qi Assigned annotations Number of assigned annotations at BAssigned annotation attribute Synonyms J E BioRS E Mapped BioRS entries Add nested Mapped BioRS entry attribute Network m m gt Knowledge H Related objects Use nested view gt Number of related objects Qi Relations Qe Relations as graph v 4 n gt Report mode H Show description Add gt gt Delete Duplicate b f Apply Discard Variables Name Figure 49 Creating a view View Items tab Assigned annotation attribute definition In the Available view items panel under Knowledge Network select the Related objects option and click the Add button Define the following information in the panel on the right and click the Apply button Table 11 View Items tab Related objects definition Oplioninthe General ub Settings OOOO Relation class Click the check box and select Functional Classification from the drop down menu Related object type Select the Related object type option Under Kind select Ontology entry from the drop down menu Under Ontology select GO from the drop down menu 33 Quick Start z gt BioXM Knowledge Management Environm
69. ontrol point of mitotic cell cycle cdc6 cell division cycle 6 homolog s cerevisiae ie GO 0008156 negative regulation of DNA replication cdc6 cell division cycle 6 s cerevisiae homolog O G0 0000166 nucleotide binding hscdc18 160 0000076 DNA replication checkpoint hscdc6 1 G0 0005737 cytoplasm cdc18 cell division cycle 18 s pombe homolog like lis GO 0000079 regulation of cyclin dependent protein kinase activity cdc6 1 6G0 0005515 protein binding cdc6 homolog 1 G0 0005524 ATP binding cdc18l 1 G0 0005634 nucleus hscdc 18 O G0 0006260 DNA replication cdc 6 O G0 0007049 cell cycle cdc i 1 60 0007067 mitosis cdc vi GO 0008285 negative regulation of cell proliferation cdc 18l 1 60 0017111 nucleoside triphosphatase activity hscdc 6 O G0 0051301 cell division hscdc vi cde 18 hscdc 18 cdc6 hscdc 6 hscdc i HsCDC6 CDC18L HsCDC18 CDC6 CDT1 Homo sapiens cdti 81620 16 O G0 0005634 nucleus double parked drosophila homolog of Oo GO 0000076 DNA replication checkpoint cdt 1 1 G0 0003677 DNA binding dna replication factor dup chromatin licensing and dna replication factor 1 ris2 the dup protein E GO 0005515 protein binding O G0 0005657 replication fork O GO 0006260 DNA replication 1 G0 0007049 cell cycle O G0 0030174 regulation of DNA dependent DNA replication initiation cdt 1 cdti the dup gene cdt1 Figure 79 Displaying the FindGenesByFunction query results 4 3 Displaying an ob
70. ooting the import 2 4 Trouble shooting the import The section lists some typical errors encountered when importing and how to overcome them 2 4 1 Error Insufficient privileges If the following type of error is displayed check that the correct scopes are set for all scope capable objects and relations in the data model ERROR Insufficient privileges See Section 1 8 Defining object type scopes and Section 1 9 Defining relation class scopes 2 4 2 Error Entry not found If an entry is not found and a variable cannot be defined the following type of error will be displayed Table parsing errors No table parsing errors occurred Import errors Line 2 ERROR Ontology entry with uid GO 0017068 not found Line 2 ERROR Ontology entry with uid GO 0000004 not found Line 2 ERROR Ontology entry with uid GO 0005554 not found Line 2 ERROR Ontology entry with uid GO 0008372 not found Line 2 ERROR Variable ontology entryl is not defined 25 Quick Start Line 4 ERROR Ontology entry with uid GO 0000004 not found Line 4 ERROR Ontology entry with uid GO 0005554 not found Line 4 ERROR Variable ontology entryl is not defined Processed lines The requested line ranges 10 are rejected and does not influence database modifications Database modifications summary No database modifications were performed If the Allow partial import option is selected such errors will be ignored during
71. operation 3 Under Available import operations select Lookup and assign BioRS and click the Add gt gt button Options for the import operation will be displayed under Tab import script Click each option listed in the 20 Quick Start table below to display the settings in the right panel After selecting the listed settings click the Apply button Table 3 Lookup and assign BioRS operation Option selected in the Settings in right panel Tab import script panel Object Select the element1 option from the drop down menu Databank Select Use constant value and EntrezGene from the drop down menu Element name Select Use constant value and D from the drop down menu ID is the primary key in the EntrezGene databank Element value Set several options e Select the Take from column radio button and C EntrezGene ID from the drop down menu Check the Split with separator check box select the Preset radio button and select the semi colon from the drop down menu Click the Edit link next to Empty invalid values processing A dialog will open Select the Skip radio button for both Empty values and Invalid values and click the OK button Skip lookup by ID Check the Assume entry exists when looking up by ID check box Setting the Skip lookup by ID option to Yes will increase the speed of the import because the BioXM system will skip creating a connection to the BioRS datab
72. orce new revision Figure 75 Editing the WebHome page 2 Open the new page by clicking FindGenesByFunction in the WebHome page amp Biomax Admin Users Log Out The BioXM Knowledge Portal Wil e G iD amp You are here BioXM F E o biomax eee Welcome to the Biomax Knowledge Portal First time users get a tour introducing the BioXM portal builder here For personal settings change your preferences Administrators if the data model has changed hit BioxmRefresh Home Sit m TY Queries of interest e FindSignalTransductionGenes e FindGenesByFunction Figure 76 Displaying the WebHome page 3 Edit the page by clicking the Edit tool to display the Foswiki editing interface We will edit the page to include the plugin for the query Executing a BioXM query that uses variables is done using the following general plugin call SBIOXM QUERY query 2 query name variables varl value var2 value The variables parameter fixes the query variable values Omitting this parameter will lead to a query form in which values can be entered by the user this is what we want to do To edit the page to include the plugin for the query without fixing the variable values enter the following text and click Save Find genes by function SBIOXM_QUERY query Find genes by function 47 Quick Start FindGenesByFunction edit v Text gt Settings gt Help Title FindGe
73. ormation Property name Attribute Synonyms Text n Relation Functtanal Classification Relation encoding Open View Edit Delete Scopes New gt Select All Ctrl A Select None Ctrl Shift A Invert Selection Ctrl R BioRS entry UNIPROT SPROT BioRS entry Entre i Undisplay Delete Attribute AlText Text Attribute ID Text Attribute AllText Text Attribute Chromosome Text Attribute CreationDate Date Attribute Crossreference Reference Attribute CurrentID Text Attribute Description Text Attribute ID Text Attribute Acc Number Text Attribute Allergen Text Attribute Aitemative Name Text Attribute Atemative Products Text Attribute Authors Author Figure 20 Opening the Object Type Scopes dialog for an element type Alternatively select Modeling Element types in the main menu to display the Element types dialog amp BioXM Knowledge Management Environment Element Types Figure 21 Opening the Object Type Scopes dialog via the Element types dialog Select a element type and click the Scopes button to display the Object Type Scopes dialog 12 Quick Start amp BioXM Knowledge Management Environment Object Type Element Gene Scopes Object Type Scopes Figure 22 Setting an element type scope Alternatively a new scope could be
74. ort and Use as default for report options P gt BioXM Knowledge Management Environment OS General View Items Report Layout Name Gene list view Allowed type s All types Object type Kind Element v v Element type Gene v Description Project H3 Public Allowed for table V Allowed for report 7 Use as default for table 7 Use as default for report Load table rows incrementally E For nested reports only Heb ok canc Figure 45 Creating a view General tab Click the View items tab The View Items interface see Figure 46 Creating a view View Items tab Object definition is similar to the import wizard with three panels Each view item is selected from the Available view items panel on the left The added item is displayed in the View items panel in the middle Depending on the item selected in the middle panel a dialog for specifying the necessary information appears in the right panel The view items will become the columns of the table in the order they are listed in the middle panel In the Available view items panel under Object Properties select the Object option and click the Add button Define the following information in the right panel and click the Apply button 29 Quick Start Table 7 View Items tab Object definition Shown by default in tables Select the Shown by default in tabl
75. ph as a placeholder for attribute value Contexts x L E a pA Variables Add gt gt Delete Duplicate Name f Figure 48 Creating a view View Items tab Mapped BioRS entry attribute definition In the Available view items panel under Annotation select the Assigned annotation attribute option and click the Add gt gt button Define the following information in the panel on the right and click the Apply button Table 10 View Items tab Assigned annotation attribute definition Name Enter Synonym in the field Shown by default in tables Select the Shown by default in tables option Select Basic information from the drop down menu Select Synonym from the drop down menu Annotation form Attribute 32 Quick Start a gt BioXM Knowledge Management Environment General View Items Report Layout i Assigned annotation attribute 2 B Object Properties R a sees QGGene Object Name Synonyms EntrezGene Mapped BioRS entries Description Sr Chromosome Mapped BioRS entry att gt QS Object type v Shown by default in tables Assigned annotation att E Sort by default Ascending Qi Static type Aliases Sorting nested view item Shape Qi Creati
76. ration Under Available import operations select Lookup or create relation and click the Add button Options for the import operation will be displayed under Tab import script Click each option listed in the table below to display the settings in the right panel After selecting the listed settings click the Apply button Table 5 Lookup or create relation operation Option selected in the Settings in right panel Tab import script panel Relation class Select the Use constant value option and Functional Classification from the drop down menu 22 Quick Start Option selected in the Settings in right panel Tab import script panel Source Select the Use result variable option and ontology entry1 from the drop down menu Select the Use result variable option and element1 from the drop down menu Create in project Select the Default for Relation Class radio button The project will be set to the default project for the relation class i e the Public project The defined operation is shown below BioXM Knowledge Management Environment Import Table Data Current Step Define Tab Import Script Tor Qi Detach annotation AT Qi Transfer annotations MY Create in project b Q Lookup and assign BioRS entry B 2 Create annotation Sannotabon1 Q Get assigned BioRS entries BD Object element1 Use result variable
77. sers to stay in touch with recent additions or changes in knowledge that should be available to the entire organization In addition the BioXM system provides a personalized work environment which supports user and project groups This environment allows researchers to focus specifically on generating knowledge in a particular scientific field This document describes the basic steps from getting started with an empty instance of the BioXM Knowledge Management Environment to creating a productive gene index knowledge base 1 Designing the data model 2 Importing data 3 Preparing views and queries 4 Preparing a BioXM web portal These steps will allow a personalized work environment to be created using tailored views smart folders and a BioXM web portal Tip For more information about the BIoXM Knowledge Management Environment see the BioXM User Manual Before using the BioXM system for the first time you may want to read the overview of the basic BioXM concepts and tools in the BioXM User Manual 1 Designing the data model The first step in building a knowledge base is to design the domain specific data model in the BioXM Knowledge Management Environment In the example use case shown here we will create a gene index knowledge base using the following seed data a table of gene names synonyms EntrezGene identifiers IDs and Gene Ontology GO classification A sketch of how we want to structure the data model is shown below
78. t Attribute AllText Text Attribute Chromosome Text Attribute CreationDate Date Attribute Crossreference Reference Attribute CurrentID Text Attribute Description Text Figure 24 Opening the Object Type Scopes dialog for a relation class Alternatively select Modeling Relation classes in the main menu to display the Relation classes dialog BioXM Knowledge Management Environment Relation Classes Functional Classification Figure 25 Opening the Object Type Scopes dialog via the Relation Classes dialog 2 Select arelation class and click the Scopes button to display the Object Type Scopes dialog 14 Quick Start BioXM Knowledge Management Environment Object Type Scopes Object Type Relation Functional Classification Scopes Project Enable Global Scope Help 0 object s ose Figure 26 Setting a relation class scope 3 Click the Enable Global Scope button After the scope is set click Close to close the dialog window 4 Complete the steps again to set the rest of the scope capable relations i e Relation encoding to have the Global Scope Upon defining the scopes the relation classes become available in the Relations repository of the project tree see Figure 16 Object types of the data model in the project tree 1 10 Saving the data model layout
79. t only option sets the BioXM system to import the entire table at once not in chunks Other import scripts in the queue will wait until the entire upload has been processed 26 Quick Start amp BioXM Knowledge Management Environment Import Table Data Current Step Import Data Table parsing errors No table parsing errors occurred Import errors No import errors occurred Processed lines The whole table is processed and accepted Database modifications summary Annotation Basic information 16 459 object s created Annotation to object assignment 16 459 object s created BioRS mapping record 16 712 object s created Element of type Gene 16 459 object s created Relation of class Functional Classification 98 453 object s created Revision annotation Basic information 16 459 object s created Figure 42 Importing data completing the import The import may take some time but you can continue working with the BioXM system as the import is processed by clicking the Put to background button To display the task again select View gt Show Background Task Manager in the main menu The Background Task Manager window will be displayed Click the task and the Task Details button to display the task Finishing the data import Click the Finish button to close the import wizard The imported elements genes will be displayed in the default Element Type View 2 Quick St
80. tach annotation No special options selected Qi Transfer annotations Q ESTE assign BioRS entry tQ Get assigned BioRS entries Try to use empty invalid values Q Assign BioRS entry Skip empty invalid values adio ast oie a v Overview Variables Name Type Value Add Data preview Click a column to select it A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid MGC129938 15E1 2 MGC 129938 15e 1 2 h O 0017068 GO 0000004 GO 0005554 G 2 GCP4 FL114797 GCP4 76P TUBGCP4 gam O 0000226 GO 0005815 GO 0000922 G 1B ABG GAB HYST2477 DKFZp686F0970 O 0016020 GO 0000004 GO 0005554 G FOX 1 HRNEP 1 FOX 1 HRNBP 1 A2BP 1 a2bp O 0000166 GO 0003723 GO 0005515 G tie Bak Next gt Finish camem Figure 35 Importing data tab import script Lookup and assign BioRS operation Under Available import operations select Lookup ontology entry and click the Add gt gt button Options for the import operation will be displayed under Tab import script Click each option listed in the table below to display the settings in the right panel After selecting the listed settings click the Apply button 21 Quick Start Table 4 Lookup ontology entry operation Option selected in the Settings in right panel Tab import script panel Ontology Select Use constant value and GO from the drop down menu Lookup by Select the Ui
81. tal The content and design of this page will vary depending on your installation but the functionality will be similar to what is described here Q Tip Administrators may need to click the BioxmRefresh link if the data model has had significant changes 4 2 Setting up a query in the BioXM web portal The BioXM web portal can be used to execute only queries that already exist in the BioXM system The principle approach is to first create queries using the BioXM query builder which we have done already create a wiki page for the query and then implement calls of the appropriate web portal plugins into the page To create a wiki page and implement the plugins complete the following steps 1 Click the Edit tool in the toolbar near the top right corner to display the Foswiki editing interface WebHome edit v Text Settings Help Title WebHome H H2 H3 HA A AAA A EEE Bae L Welcome to the Biomax Knowledge Portal First time users get a tour introducing the BioXM portal builder WebHomeFirstTimeStart here br For personal settings change your UserPreferences preferences lt br gt Administrators if the data model has changed hit BioxmRefresh v Save B Save and Continue Preview 3 Cancel Force new revision Figure 70 Foswiki editing interface Here we can change the content of the WebHome page the BioXM web portal entry page using Foswiki markup 2 First we will create a
82. the import See Section 2 5 Completing the import 2 5 Completing the import If there are no problems upon simulating the import we can proceed to the actual data import 1 Openthe Choose processing policy step of the import wizard In the import wizard click the Back button Alternatively start a new import wizard by selecting File gt Import Table in the main menu and using the existing Import gene index table script Click the Next button until the Choose processing policy step of the wizard is displayed 2 Choose a processing policy to perform the import 7 gt BioXM Knowledge Management Environment Import Table Data Current Step Choose Processing Policy Allow partial import Commit changes for errorless import operations by small portions Allow complete import only Do not commit any changes if any errors were found Simulate import Do not commit any changes even on successfull import Stop after the specified number of errors 1000 Process only lines Comma separated list of ranges each in the form from to either end may be omitted Example 10 20 30 40 50 4 Produce import log Record all import operation activity for each table row Data preview A Gene Name B Synonyms C EntrezGene ID D GO Ontology entry Uid 2 15E1 2 Homo sapiens MGC 129938 15E 1 2 MGC 129938 15e 1 2 h 283459 so 006450 3 76P
83. tion class from Element Gene to Element Protein from the menu The New relation class dialog will appear Quick Start gt BioXM Knowledge Management Environment New Relation Class General Definition Representation Name encodi Description Activate new relation dass h Figure 6 Adding a new relation class 3 Inthe General tab enter encoding in the name field In the Definition tab enter encodes in the Forward Name field and is encoded by in the Backward Name field We will use the default settings in the Representation tab Click the OK button The Relation encoding will appear in the data model graph P gt Data Model Graph BioXM E ww liom EE mm 8 aa ge Element Gene Relation encoding Property name Property description Figure 7 New relation class in the data model 1 5 Adding an annotation form To add some basic information including synonyms to the genes and proteins we will add a new annotation form called Basic information to the data model and associate it with the gene and protein elements 1 Right click on the whitespace in the data model graph to display the context sensitive menu Select New Annotation form from the drop down menu The Create new annotation form dialog will be displayed Data Model Graph B
84. ts cc cece ccc e cece ee ee ee eee tees mme me me eme menn ns 37 23 9 Hedelmibd the lel y raeino sede aor pen E r caue Vom vage utes To lean Eno Upad nba ereraa 39 3 6 Saving the query and creating a smart folder cc cece cece cece eee ee eee eeeeaeeaeeeeeeeeeeeeenees 40 Sc Eig he smat Todes seien sued uei d exacts acea teusice beau as ein sen Xat is cue ML oO DOE SUC TAN es 40 4 Preparing a BIoXM web portal cccccecc ccc e ee eee eee e ee eee Imm me nm me menses nsn rne as 43 4 1 Logging into a BioXM web portal co assast tate pae a Eid eene ceu dac texta aider aetas 43 4 2 Setting up a query in the BiOXM web portal cccccceceeeeeeseeeeeeeeeseeaeeaeeuseeaeeaneenenas 44 4 3 Displaying an object report in the web portal ccccccece eee eee eee e eee eeeeeaeeeeeeeeeaeeaneeneeaes 49 Be AG melio PNEU UI IDIPECDPT ECEnn EPUM 54 6 LOGOINGS OUI EL IN UT 54 6 1 Logging out of the BioXM client application cccc ccc e eee eee eee sees eeeeeeeeeeeeeeeegnenanens 54 6 2 Logging out of the BiOXM web portal cccecceccene eee eeeeeeeeeeeeeeeeeeaeeeeeeaeeeseeaneaneunenas 54 Quick Start The BioXM Knowledge Management Environment is a project centered distributed platform that facilitates communication and collaboration in a research environment The BioXM system provides a central inventory of information describing a particular area of research making it easy for u
85. txt Browse File type Autodetect Plain text Excel SpreadsheetML Open Document Figure 30 Importing data choosing the data source 3 Dothe following to define the physical layout of the table A preview of the data is displayed at the bottom of the window 1 Under Columns click the Separated columns radio button Specify the column separator under Separator by selecting the Preset option and Tab from the drop down menu 2 Under Columns Text qualifier select the None radio button 3 Under Header select 0 lines to skip and click the Recognize table header option 4 Under Encoding select UTF 8 to accommodate special characters 5 Click the Next button to continue to the Choose Script Kind step of the import wizard 17 Quick Start Y BioXM Knowledge Management Environment Import Table Data Current Step Define Physical Layout Treat consecutive separators as one Fixed number of columns Fixed width columns Comma separated list of column widths the last may be to take maximum space B Synonyms C EntrezGene ID D GO Ontology entry Uid 129938 15E 1 2 MGC 129938 283459 O 0017068 GO 0000004 GO 0 CP4 FLJ14797 GCP4 76P TUBG 27229 O 0000226 GO 0005815 GO 0 A 1B ABG GAB HYST2477 DKFZp 1 O 0016020 GO 0000004 GO 0 OX 1 HRNBP 1 FOX 1 HRNEBP 1 A2 54715 O 0000166 GO 0003723 GO 0 dkfzp779b086 alpha 2 macroglo
86. ults 1 Click the Next gt button to display the query results 3 7 Quick Start Find by advanced query BioXM View E Gene list view 2 Gene v 7 Search Gene Synonyms EntrezGene Chromosome GO AARSD1 Homo sa 2744 80755 17 L1 GO 0007165 signal transduction AARSD1 GO 0050220 prostaglandin E synthase a Lem G0 0000781 chromosome telomeric re Igc2744 L G0 0051082 unfolded protein bindin barsd1 O GO 0004813 alanine tRNA ligase activity barsd i L GO 0006419 alanyl tRNA aminoacylation alanyl trna synthetase domain i GO 0000166 nucleotide binding containing i i GO 0005524 ATP binding garsd i O GO 0006412 translation a G0 0016874 ligase activity containing alanyl trna synthetase domain containing 1 yl trna synthetase domain ABR Homo saan e 29 17 GO 0005096 GTPase activator activity oo 3 GO 0005622 intracellular LJ G0 0035023 requlation of Rho protein sig ee aed 0 G0 0005089 Rho quany nucleotide exch egion related protein isoform L GO 0007165 signal transduction b L GO 0007264 small GTPase mediated sig abr fj45954 mdb active breakpoint cluster ACCN2 Homo sap 41 12 0 GO 0005887 integral to plasma membrat 2 GO 0007165 signal transduction oo 0 G0 0008810 transport IACCN2 L1 GO 0005515 protein binding i L GO 0005216 ion channel activity Figure 58 Creating a query displaying query results
87. using the BioRS system BioRS databanks Genes will be mapped to the EntrezGene databank and proteins will be mapped to the UniProt Swiss Prot databank Quick Start l Right click on the whitespace in the data model graph to display the context sensitive menu Select New gt BioRS databank The New BioRS Databank dialog will be displayed l BioXM Knowledge Management Environment 2S BioRS Connection BioRS Databank EntrezGene Choose Name EntrezGene Description V Precache linked entries Lox J Figure 13 Adding a new BioRS databank 2 Click the Choose button to display the BioRS connection options select a BioRS connection by clicking it in the list and click OK 3 Likewise click the Choose button to display the available BioRS databanks select a databank and click OK For this use case select the EntrezGene databank 4 Click the OK button in the New BioRS Databank dialog The EntrezGene databank will appear in the data model graph 2 Using the select tool assign the gene element type to the databank by dragging and dropping the BioRS entry EntrezGene to the Element Gene and selecting the Assign Element Gene to BioRS databank EntrezGene option from the context sensitive menu Quick Start P Data Model Graph BioXM Layout Graphviz directed v n Annotation Basic information Property name Attribute Synony
88. w Items tab Related objects definition Before closing the dialog we will reorder the view items so the Synonyms are shown in the second column of the Gene list view table Select the Synonyms item in the middle panel and click the arrow up button 4 to put it in the second position in the panel The view items defined become the columns of the table in the order they are listed in the middle panel 3 gt BioXM Knowledge Management Environment Edit View General View Items Report Layout Available view items Mapped BioRS entries Object Properties Name Name EntrezGene e Caption um Synonyms Assigned annotation att Q Description See e Object Mapped BioRS entries Object type Mapped BioRS entry att Static type Related objects GO en Q Aliases Sorting nested view item ee Shape Qi Creation time Qi Creation user name gt Last modification time BioRS databank Q Last modification user name Annotation Q8 EntrezGene i QU Assigned annotations Number of assigned annotations Qi Assigned annotation attribute Use nested view BioRS Mapped BioRS entries i Mapped BioRS entry attribute Knowledge Network Z BRelated objects EE Qe Number of related objects V Shown by default in tables Sort by default Ascending Report mode t Qi Relations t Qi Relations as graph 4 p
89. way induced by DNA damage that blocks cell cycle progression in G1 50 0000161 IAPKKK cascade involved in osmosensory signaling APKKK cascade involved in signal transduction in response to change in osmotic conditions 50 0000750 omone dependent signal transduction involved in A signal transduction process resulting in the relay amplification or dampening of a signal 50 0000757 i transduction involved in conjugation with mutual A signal transduction process resulting in the relay amplification or dampening of a signal 560 0007093 itotic cell cycle checkpoint 50 0007094 itotic cell cycle spindle assembly checkpoint 50 0007095 ie cell cycle G2 M transition DNA damage checkpoint 0 0033313 eiotic cell cycle checkpoint 0 0033314 itotic cell cycle DNA replication checkpoint 50 0033315 meiotic cell cycle DNA replication checkpoint A signal transduction based surveillance mechanism that ensures accurate chromosome replication A signal transduction based surveillance mechanism that ensures the fidelity of cell division by A signal transduction based surveillance mechanism that acts during a mitotic cell cyde t to ensure signal transduction based surveillance mechanism that ensures accurate chromosome replication A signal transduction based surveillance mechanism that acts during a mitotic cell cycle and A signal transduction based surveillance mechanism that acts during a meiotic cell cycle and DDDDDDDDDDO 8 515 I8 8155 IS I
90. wledge Management Environment see the BioXM User Manual or the BIoXM online help To open the BioXM online help select Helo Online Help from the BioXM main menu The BioXM online help will open in a new window 6 Logging out 6 1 Logging out of the BioXM client application You can log out of the BioXM client application by selecting one of the following options from the main menu File Log Out log out the current user without exiting the BioXM application you can subsequently log in again with the same or different user name File gt Exit BioXM log out the current user and exit the BioXM application Additionally you can log out and exit the BioXM application by closing the main application window A confirmation dialog will be displayed before you are logged out and the application closes 6 2 Logging out of the BioXM web portal You can log out of the BioXM web portal by clicking the Log Out link in the top right corner 54
91. ypes of the data model in the project tree The Gene and Protein element types are found in the Elements repository The Basic information annotation form is found in the Annotation repository 13 Quick Start 1 9 Defining relation class scopes Next we will define the scopes for the relation classes Like scopes for objects relation class scopes define the project s in which a relation class can be used Relation classes set to the Global Scope setting can be created within any project including any new projects that may be created 1 Inthe data model graph right click a relation e g Relation Functional Classification and select Scopes from the context sensitive menu amp Data Model Graph BioXM EI Align 100 Layout GraphViz directed m v hi a State My Model amp X m Annotation assignment Relation i ia Classification Open View Edit Delete relation configuration s Delete n encoding Scopes Add Point Select All Select None Invert Selection Undisplay Ctrl A Ctrl Shift A Ctrl R Delete Q BioRS entry UNIPROT SPROT Attribute AllText Text Attribute ID Text Attribute Acc Number Text Attribute Allergen Text Attribute Alternative Name Text Attribute Atemative Products Text Attribute Authors Author DMtriburte Distanhnalans Taxt BioRS entry EntrezGene Attribute ID Tex

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